BI0409 Chemoinformatics Laboratory
BI0409 CHEMOINFORMATICS LAB MANUAL Offered to III YEAR B.TECH BIOINFORMATICS
DEPARTMENT OF BIOINFORMATICS SCHOOL OF BIOENGINEERING SRM UNIVERSITY KATTANKULATHUR
Sub. Code/Sub.Title: BI0409/ Chemoinformatics Laboratory Sem/Year: VII/IV
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Sub. Code/Sub.Title: BI0409/ Chemoinformatics Laboratory Sem/Year: VII/IV
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Knowledge about Chemical Databases
Aim: To study & to analyze the information from the various chemical databases available on the World Wide Web.
Description:
Chemical data are highly complex and interrelated. Vast amount of chemical information needs to be stored organized and indexed so that the information can be retrieved and used. There are five major types of databases namely PubChem, ZINC, ChemBank, PDBeChem, ChemExper.
Procedure:
1. Open web browser and type the web address of the required database. 2. Explore the database and analyze various information available in the database. 3. Use the tools provided by the databases. 4. Save the output into a separate folder.
1.PubChem
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URL: http://pubchem.ncbi.nlm.nih.gov/
PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative.
PubChem includes substance information, compound structures, and BioActivity data in three primary databases, Pcsubstance, Pccompound, and PCBioAssay, respectively. • Pcsubstance contains more than 69 million records. You can check the count of substance records as of today. • Pccompound contains more than 27 million unique structures. You can check the count of compound records as of today. • PCBioAssay contains more than 434,000 BioAssays. Each BioAssay contains a various number of data points. You can check the count of BioAssay records as of today.
The Substance/Compound database, where possible, provides links to BioAssay description, literature, references, and assay data points. The BioAssay database also includes links back to the Substance/Compound database. PubChem is integrated with Entrez, NCBI's primary search engine, and also provides compound neighboring, sub/superstructure, similarity structure, BioActivity data, and other searching features.
PubChem contains substance and BioAssay information from a multitude of depositors. You can check the PubChem data source status as of today.
PubChem Substance Database
The PubChem substance database contains chemical structures, synonyms, registration IDs, description, related urls, database cross-reference links to PubMed, protein 3D structures, and biological screening results. If the contents of a chemical sample are known, the description includes links to PubChem Compound.
PubChem Compound Database
The PubChem Compound Database contains validated chemical depiction information that is provided to describe substances in PubChem Substance. Users can perform a term/keyword search in a same manner as for substance database. In addition, the PubChem compound database also provides a chemical property search.
Examples:
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Molecular weight search: compounds have molecular weight between 100 and 200.Enter 100:200[mw] or 100:200[molecular weight] in the Search textbox and press the Go button. • XLogP search: compounds have XLogP between 2.3 and 2.4. Enter 2.3:2.4[xlogp] in the Search textbox and press the Go button. • Heavy atom count search: compounds contain 8 heavy atoms. Enter 8[heavyatomcount] in the Search textbox and press the Go button. Chemical property range searches: substances do not violate the "Lipinski Rule of 5". In the Chemical Property Search section: For the Molecular Weight (MW) range, type 0 and 500 in the from and to text boxes, respectively. or the Hydrogen Bond Donor Count (HBD) range, type 0 and 5 in the from and to text boxes, respectively. or the Hydrogen Bond Acceptor Count (HBA) range, type 0 and 10 in the from and to text boxes, respectively. or the XLogP range, type -5 and 5 in the from and to text boxes, respectively. Push the Go button in the top Search bar.BioActivity Analysis links for reported "Chemical Probes", "Active" compounds, and "Tested" compounds are shown with the icons. The home page of PubChem can be seen as follows:
Output:
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Query Examples:
• Molecule synonym search
Which substances have "methotrexate" as a part of their molecule name?
Simply enter methotrexate in the Search textbox on the PubChem homepage or Entrez search page and press the Go button. You will get all substances with the synonym methotrexate and/or with any other keyword methotrexate.
Or enter methotrexate [synonym] in the Search textbox and press the Go button.
Note: the term in the brackets "[]", such as "[synonym]", is an index field name or alias. For more information about index searches, please see PubChem Indexes and Index Search.
Which substances have "3'-Azido-3'-deoxythymidine" as their molecule name?
Enter "3'-Azido-3'-deoxythymidine" (including the quotes) in the Search textbox and press the Go button.
2. ZINC
URL: http://zinc.docking.org/
It is a free database of commercially-available compounds for virtual screening.
Virtual screening (VS) is a computational technique used in drug discovery research. It involves the rapid in-silico assessment of large libraries of chemical structures in order to identify those structures that most likely to bind to a drug target, typically a protein receptor or enzyme.
ZINC is provided by the Shoichet Laboratory in the Department of Pharmaceutical Chemistry at the University of California, San Francisco (UCSF).
The home page of ZINC can be viewed as follows:
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3. ChemBank
URL: http://chembank.broadinstitute.org/
ChemBank is a public, web-based informatics environment created by the Broad Institute's Chemical Biology Program and funded in large part by the National Cancer Institute's Initiative for Chemical Genetics (ICG). Currently, ChemBank stores information on hundreds of thousands of small molecules and hundreds of biomedically relevant assays that have been performed at the ICG in collaborations involving biomedical researchers worldwide.
We Can:-
1. Find Small Molecules
• by substructure: Search compound collection by substructure (may be specified via a SMILES or SMARTS string, or drawn with JME Molecular Editor). Sub. Code/Sub.Title: BI0409/ Chemoinformatics Laboratory Sem/Year: VII/IV
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• by similarity: Search compound collection by similarity to a structure (may be specified via a SMILES string, or drawn with JME Molecular Editor). • using descriptors: Filter compound collection using calculated molecular descriptor values. • by assay: Find compounds scoring as "hits" in biological assays. • by function: Find compounds with known biochemical interactions, therapeutic uses, or molecular functions. • by chemist: Find compounds made by a particular chemist, or sold by a particular vendor. • by molecule name: Find compounds with a particular name, or containing a part of a name. • by user list
The home page of ChemBank can be viewed as follows:
4. PDBeChem
URL: http://www.ebi.ac.uk/msd-srv/msdchem/cgi-bin/cgi.pl
Introduction
The Chemical component dictionary service provides web access to the "Chemical Component Dictionary" of the wwPDB as this is loaded in the PDBe database at EBI. Sub. Code/Sub.Title: BI0409/ Chemoinformatics Laboratory Sem/Year: VII/IV
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How to search with PDBeChem
There is a wide range of possibilities for searching and exploring the dictionary. • Code: This is the PDB 3 letter code for the ligand (i.e. ATP). You may also select the "like" operator with a wildcard expression ('*' means any characters and '.' means one character) For example *TP will match most triphospate ligands. • Molecule name: An expression or word that is part of any of known molecule name (standard name, common name, systematic name). The special character '*' matches a sequence of any characters and '.' matches any single character. Examples: 'amino' • Formula: An expression that sets range constraints for the number of atoms from each element. The value that you have to provide is of the form [
- 'CL3 N0' find molecules with exactly 3 Clorines and no nitrogens
• Non stereo smile: For structure based searches. By clicking on the edit button, a form appears that will allow you to specify a molecule or a molecule segment by using one of the three options:
- Draw the molecule using the JME Molecular editor
- Upload a standard chemical file like Mol2,Sdf,PDB e.t.c. in the JME editor. You may specify any file types and formats accepted by the CACTVS system
- Give the standard code (i.e. ATP) of a ligand that already exists in the database in order to be loaded on the JME editor.
After you load a ligand you may also modify it. For example if you are looking for ligands similar to ATP you may load ATP on the JME editor and then remove some atoms and bonds, keeping just the substructure you are interested in. As soon as a molecule or molecule segment is specified then you may use it to search the dictionary using one of the following operators:
- contains: Find all the ligands that whose graph contains the molecule specified as a subgraph. Please be patient since this operation may take a few (2-4) minutes in the worst case.
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- is contained: Find all the ligands that are contained as subgraphs in the graph of the specified molecule. Please be patient since this operation may take a few (2-4) minutes in the worst case.
All these search operations ignore sterechemistry. This means that a molecule will also match its stereoisomers. Additionally aromatic bonds are treated as single-double. This means that in the case of aromatic rings etc, there may be also some false positives.
Fragments: Similar to formula search but now the search items are not chemical elements but chemical fragments. An expression sets range constraints for the number of occurences from each fragment. The value that you have to provide is of the form [
The home page can be viewed as follows:
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5. ChemExper
URL: http://:www.chemexper.com/
Goal of the ChemExper Chemical Directory
The goal of this project is to create a common and freely accessible database of chemicals over the internet. This database contains chemicals with their physical characteristics. Everybody can submit chemical information and retrieve information with a Web browser.
Finding chemicals in the ChemExper Chemical Directory done by:
Entering a name, molecular formula, cas number or SMILES
The home page can be seen as follows:
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RESULT: Knowledge about all the five databases was obtained.
Ex no:2 Date:
Knowledge of Various Chemical File Formats
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1. SMILES
URL: http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html SMILES - A Simplified Chemical Language
SMILES (Simplified Molecular Input Line Entry System) is a line notation (a typographical method using printable characters) for entering and representing molecules and reactions. Some examples are:
SMILES Name SMILES Name CC ethane [OH3+] hydronium ion O=C=O carbon dioxide [2H]O[2H] deuterium oxide
SMILES contains the same information as might be found in an extended connection table. The primary reason SMILES is more useful than a connection table is that it is a linguistic construct, rather than a computer data structure. SMILES is a true language, albeit with a simple vocabulary (atom and bond symbols) and only a few grammar rules. SMILES representations of structure can in turn be used as "words" in the vocabulary of other languages designed for storage of chemical information (information about chemicals) and chemical intelligence (information about chemistry).
Atoms Atoms are represented by their atomic symbols: this is the only required use of letters in SMILES. Each non-hydrogen atom is specified independently by its atomic symbol enclosed in square brackets, [ ]. The second letter of two-character symbols must be entered in lower case. Elements in the "organic subset" B, C, N, O, P, S, F, Cl, Br, and I may be written without brackets if the number of attached hydrogens conforms to the lowest normal valence consistent with explicit bonds. C methane (CH4) O water (H2O)
[S] elemental sulfur [Au] elemental gold [H+] proton [Fe+2] iron (II) cation [OH-] hydroxyl anion [Fe++] iron (II) cation [OH3+] hydronium cation [NH4+] ammonium cation
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Bonds Single, double, triple, and aromatic bonds are represented by the symbols -, =, #, and :, respectively. Adjacent atoms are assumed to be connected to each other by a single or aromatic bond (single and aromatic bonds may always be omitted).
CC ethane (CH3CH3) C=C ethene (CH2=CH2) C#N hydrogen cyanide (HCN) [H][H] molecular hydrogen (H2)
Branches Branches are specified by enclosing them in parentheses, and can be nested or stacked. In all cases, the implicit connection to a parenthesized expression (a "branch") is to the left.
CCN(CC)CC Triethylamine
Cyclic Structures Cyclic structures are represented by breaking one bond in each ring. The bonds are numbered in any order, designating ring opening (or ring closure) bonds by a digit immediately following the atomic symbol at each ring closure.
Disconnected Structures Disconnected compounds are written as individual structures separated by a "." (period). The order in which ions or ligands are listed is arbitrary. There is no implied pairing of one charge with another, nor is it necessary to have a net zero charge.
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Isomeric SMILES The SMILES rules used to specify isotopism, configuration about double bonds, and chirality are described below:
1. Isotopic Specification Isotopic specifications are indicated by preceding the atomic symbol with a number equal to the desired integral atomic mass. An atomic mass can only be specified inside brackets. [12C] carbon-12 [13C] carbon-13
2.Configuration Around Double Bonds Configuration around double bonds is specified by the characters / and \ which are "directional bonds" and can be thought of as kinds of single or aromatic (eg. default) bonds. These symbols indicate relative directionality between the connected atoms, and have meaning only when they occur on both atoms which are double bonded.
F/C=C/F F/C=C\F F\C=C\F F\C=C/F
3. Configuration Around Tetrahedral Centers The simplest and most common kind of chirality is tetrahedral; four neighbor atoms are evenly arranged about a central atom, known as the "chiral center". If all four neighbors are different from each other in any way, mirror images of the structure will not be identical. The two mirror images are known as "enantiomers" and are the only two forms that a tetrahedral center can have. If two (or more) of the four neighbors are identical to each other, the central atom will not be chiral (its mirror images can be superimposed in space). In SMILES, tetrahedral centers may be indicated by a simplified chiral specification (@ or @@) written as an atomic property following the atomic symbol of the chiral atom. If a chiral specification is not present for a chiral atom, its chirality is implicitly not specified. L-alanine D-alanine N[C@@H](C)C(=O)O L-alanine N[C@H](C)C(=O)O D-alanine
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2. Molfiles
Expansion: MDL Molfile
Use:
It is used for holding information about the atoms, bonds, connectivity and coordinates of a molecule.
Lab:
An MDL Molfile is a file format created by MDL (now Symyx).
Representation:
The molfile consists of some header information, the Connection Table (CT) containing atom info, then bond connections and types, followed by sections for more complex information.
Advantage:
The molfile is sufficiently common that most, if not all, cheminformatics software systems/applications are able to read the format.
Example: Benzene
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3. SDF
Expansion: "SDF" stands for structure-data file.
Use: It is intended especially for structural information.
Developer: SDF is one of a family of chemical-data file formats developed by MDL.
Advantage: Multiple data items are permitted on multiple lines.
Representation:
Multiple compounds are delimited by lines consisting of four dollar signs ($$$$). A feature of the SDF format is its ability to include associated data.
Example: Benzene
4. International Chemical Identifier
Expansion: The IUPAC International Chemical Identifier Sub. Code/Sub.Title: BI0409/ Chemoinformatics Laboratory Sem/Year: VII/IV
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Use: It is used to provide a standard and human-readable way to encode molecular information and to facilitate the search for such information in databases and on the web.
Developer: Developed by IUPAC and NIST during 2000–2005, the format and algorithms are non- proprietary and the software is freely available under the open source LGPL license.
Advantage:
They can express more information than the simpler SMILES notation and differ in that every structure has a unique InChI string which is important in database applications.
Algorithm:
The InChI algorithm converts input structural information into a unique InChI identifier in a three-step process: normalization (to remove redundant information), canonicalization (to generate a unique number label for each atom), and serialization (to give a string of characters).
Example: Benzene InChI=1/C6H6/c1-2-4-6-5-3-1/h1-6H
RESULT: The knowledge about all the above chemical file formats were obtained.
Ex.No:3 Date:
Retrieval of Information about given Chemical Compounds
AIM: To obtain information about the given chemical compounds.
1. Tolmetin 2. Naproxen 3. Diclofenac 4. Ketoprofen 5. Aspirin
Compound PubChem ZINC ChemBank PDBeChem ChemExper Tolmetin CID 5509 2191 ChemBankID: No results C07149 865 Tolmetin Naproxen CID 103450 ChemBankID: No results RN: 22204-53-1
156391 907391 MF: C14H14O3
MW: 230.26336
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Diclofenac CID 3033 1281 ChemBankID: DIF RN: 15307-86-5
915 MF: C14H11NO2Cl2
MW: 296.15284
Ketoprofen CID 3825 2272 ChemBankID: AKY MF: C16H1403 1209 ERT NGM NGU Aspirin CID 2244 53 ChemBankID: AIN MF: C9H804 1171 S3B
THE CHEMICAL FILE FORMATS AVAILABLE IN PUBCHEM FOR THE ABOVE CHEMICAL COMPOUNDS ARE:
TOLMETIN:
BioAssay Results:
Tested in BioAssays: All: 23 BioActivity Summary: This Compound with Similar Compounds
Depositor-Supplied Synonyms: (Total: 74) tolmetin Tolectin Tolmetine Tolmetinum Tolmetina Tolmetino Tolmetina [DCIT] Tolmetine [INN-French] Tolmetinum [INN-Latin] Tolmetino [INN-Spanish]
Properties Computed from Structure:
Molecular Weight 257.2845 [g/mol]
Molecular Formula C15H15NO3 XLogP3 2.8 H-Bond Donor 1 H-Bond Acceptor 3 Rotatable Bond Count 4 Tautomer Count 15 Exact Mass 257.105193 MonoIsotopic Mass 257.105193 Topological Polar Surface Area 59.3 Sub. Code/Sub.Title: BI0409/ Chemoinformatics Laboratory Sem/Year: VII/IV
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Heavy Atom Count 19 Formal Charge 0 Complexity 347 Isotope Atom Count 0 Defined Atom StereoCenter Count 0 Undefined Atom StereoCenter Count0 Defined Bond StereoCenter Count 0 Undefined Bond StereoCenter Count 0 Covalently-Bonded Unit Count 1
Descriptors Computed from Structure:
IUPAC Name: 2-[1-methyl-5-(4-methylbenzoyl)pyrrol-2-yl]acetic acid Canonical SMILES: CC1=CC=C(C=C1)C(=O)C2=CC=C(N2C)CC(=O)O InChI: InChI=1S/C15H15NO3/c1-10-3-5-11(6-4-10)15(19)13-8-7-12(16(13)2)9-14(17) 18/h3-8H,9H2,1-2H3,(H,17,18) InChIKey: UPSPUYADGBWSHF-UHFFFAOYSA-N
Compound Information:
CID 5509 Create Date: 2005-03-25
Related Compounds: Same, Connectivity: 2 Links
Similar Compounds: 250 Links Similar Conformers: 179 Links View Conformers
Substance Information:
Substances: All: 118 Links Same structure: 47 Links Mixture: 71 Links
Category: [for same structure substances] Biological Properties: 35 Links BIDD ( 1 ) SID 93166626 - External ID: BIDD:GT0468 ChEBI ( 1 ) SID 85417020 - External ID: CHEBI:218617 ChemBank ( 25 ) ChemSpider ( 1 ) SID 29224552 - External ID: 5308 Sub. Code/Sub.Title: BI0409/ Chemoinformatics Laboratory Sem/Year: VII/IV
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DiscoveryGate ( 1 ) SID 8153389 - External ID: 5509 DrugBank ( 1 ) SID 46507060 - External ID: DB00500 ICCB-Longwood/NSRB Screening Facility, Harvard Medical School ( 1 ) SID 92309062 - External ID: HMS2090D06 LeadScope ( 1 ) SID 50037570 - External ID: LS-136618 NextBio ( 1 ) SID 50576757 - External ID: 5509 NovoSeek ( 1 ) SID 57322816 - External ID: 5509 xPharm ( 1 ) SID 7980812 - External ID: 9647
Chemical Reactions: 1 Link ChemSpider ( 1 ) SID 29224552 - External ID: 5308
Journal Publishers: 1 Link Thomson Pharma ( 1 ) SID 14774544 - External ID: 00005252
Metabolic Pathways: 2 Links KEGG ( 2 ) SID 9358 - External ID: C07149 SID 7849414 - External ID: D02355
NIH Molecular Libraries: 2 Links Broad Institute ( 2 ) SID 85789564 - External ID: BRD-K82562631-236-02-0 SID 85787331 - External ID: BRD-K82562631-325-03-9
Physical Properties: 4 Links ChemSpider ( 1 ) SID 29224552 - External ID: 5308 DrugBank ( 1 ) SID 46507060 - External ID: DB00500 NIST ( 1 ) SID 10451692 - External ID: 1839471634 NIST Chemistry WebBook ( 1 ) SID 10516103 - External ID: 1839471634
Substance Vendors: 3 Links Ambinter ( 1 ) SID 95258113 - External ID: AmbagaB154345 Hangzhou Trylead Chemical Technology ( 1 ) SID 49836361 - External ID: TL8006558 MolPort ( 1 ) Sub. Code/Sub.Title: BI0409/ Chemoinformatics Laboratory Sem/Year: VII/IV
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SID 91750457 - External ID: MolPort-003-987-733
Theoretical Properties: 3 Links ChemDB ( 1 ) SID 4720233 - External ID: 6516061 ChemSpider ( 1 ) SID 29224552 - External ID: 5308 DrugBank ( 1 ) SID 46507060 - External ID: DB00500
Toxicology: 1 Link ChemIDplus ( 1 ) SID 175197 - External ID: 026171233
Canonical SMILES: CC1=CC=C(C=C1)C(=O)C2=CC=C(N2C)CC(=O)O
InChI: InChI=1S/C15H15NO3/c1-10-3-5-11(6-4-10)15(19)13-8-7-12(16(13)2)9-14(17)18/h3- 8H,9H2,1-2H3,(H,17,18)
SDF: 5509 -OEChem-07131002122D
34 35 0 0 0 0 0 0 0999 V2000 2.0000 0.6506 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.6227 3.7846 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.8038 2.0621 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.8366 1.6451 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 4.8147 1.8530 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7320 0.6506 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3147 0.9870 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6456 0.2438 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2215 2.7666 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8660 0.1506 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0934 2.3142 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8660 -0.8494 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7320 -1.3494 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0000 -1.3494 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8660 -2.8494 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7320 -2.3494 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0000 -2.3494 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.2160 2.8711 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8660 -3.8494 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9313 0.9222 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 4.7745 -0.3626 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 5.2647 3.3850 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 4.6199 2.9165 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5083 2.7750 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
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2.6327 2.7291 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 2.6786 1.8535 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2690 -1.0394 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4631 -1.0394 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2690 -2.6594 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4631 -2.6594 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 2.2460 -3.8494 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 2.8660 -4.4694 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 3.4860 -3.8494 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 7.2393 3.8494 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 1 10 2 0 0 0 0 2 18 1 0 0 0 0 2 34 1 0 0 0 0 3 18 2 0 0 0 0 4 5 1 0 0 0 0 4 6 1 0 0 0 0 4 11 1 0 0 0 0 5 7 2 0 0 0 0 5 9 1 0 0 0 0 6 8 2 0 0 0 0 6 10 1 0 0 0 0 7 8 1 0 0 0 0 7 20 1 0 0 0 0 8 21 1 0 0 0 0 9 18 1 0 0 0 0 9 22 1 0 0 0 0 9 23 1 0 0 0 0 10 12 1 0 0 0 0 11 24 1 0 0 0 0 11 25 1 0 0 0 0 11 26 1 0 0 0 0 12 13 2 0 0 0 0 12 14 1 0 0 0 0 13 16 1 0 0 0 0 13 27 1 0 0 0 0 14 17 2 0 0 0 0 14 28 1 0 0 0 0 15 16 2 0 0 0 0 15 17 1 0 0 0 0 15 19 1 0 0 0 0 16 29 1 0 0 0 0 17 30 1 0 0 0 0 19 31 1 0 0 0 0 19 32 1 0 0 0 0 19 33 1 0 0 0 0 M END $$$$
NAPROXEN:
BioAssay Results:
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Tested in BioAssays: All: 223 Inactive: 93 BioActivity Summary: This Compound with Similar Compounds
AID: 2291 Source: The Scripps Research Institute Molecular Screening Center Fluorescence polarization-based Maybridge primary biochemical high throughput screening assay to identify inhibitors of Protein Phosphatase Methylesterase 1 (PME-1).
AID: 434982 Source: The Scripps Research Institute Molecular Screening Center Cell-based luminescence-based Maybridge primary high throughput screening assay to identify agonists of NOTCH
AID: 346087 Source: ChEMBL Inhibition of IgE-specific antigen-induced LBT4 release in rat MC9 cells
AID: 2551 Source: NCGC qHTS for inhibitors of ROR gamma transcriptional activity more ...
Protein Structures MMDB ID: 62694 PDB ID: 2VDB Structure Of Human Serum Albumin With S-Naproxen And The Ga Module Taxonomy: Homo sapiens
Depositor-Supplied Synonyms: (Total: 198)
NAPROXEN Naprosyn Equiproxen Naproxene Laraflex Calosen Reuxen Bonyl Axer d-Naproxen
Properties Computed from Structure:
Molecular Weight 230.25916 [g/mol]
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Molecular Formula C14H14O3 XLogP3 3.3 H-Bond Donor 1 H-Bond Acceptor 3 Rotatable Bond Count 3 Exact Mass 230.094294 MonoIsotopic Mass 230.094294 Topological Polar Surface Area 46.5 Heavy Atom Count 17 Formal Charge 0 Complexity 277 Isotope Atom Count 0 Defined Atom StereoCenter Count 1 Undefined Atom StereoCenter Count0 Defined Bond StereoCenter Count 0 Undefined Bond StereoCenter Count 0 Covalently-Bonded Unit Count 1
Descriptors Computed from Structure:
IUPAC Name: (2S)-2-(6-methoxynaphthalen-2-yl)propanoic acid Canonical SMILES: CC(C1=CC2=C(C=C1)C=C(C=C2)OC)C(=O)O Isomeric SMILES: C[C@@H](C1=CC2=C(C=C1)C=C(C=C2)OC)C(=O)O InChI: InChI=1S/C14H14O3/c1-9(14(15)16)10-3-4-12-8-13(17-2)6-5-11(12)7-10/h3- 9H,1-2H3,(H,15,16)/t9-/m0/s1 InChIKey: CMWTZPSULFXXJA-VIFPVBQESA-N
Compound Information:
CID 156391Create Date: 2005-06-29
Related Compounds: Same, Connectivity: 9 Links Same, Stereochemistry: 4 Links Same, Isotopes: 3 Links
Similar Compounds: 891 Links Similar Conformers: 344 Links View Conformers
Substance Information:
Substances:
All: 233 Links Sub. Code/Sub.Title: BI0409/ Chemoinformatics Laboratory Sem/Year: VII/IV
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Same structure: 63 Links Mixture: 170 Links
Category: [for same structure substances] Biological Properties: 38 Links BIDD ( 1 ) SID 93166220 - External ID: BIDD:GT0062 CC_PMLSC ( 1 ) SID 22391409 - External ID: UPCMLD-DP001:001 ChEBI ( 2 ) SID 85350591 - External ID: CHEBI:151056 SID 93165414 - External ID: CHEBI:7476 ChemBank ( 22 ) ChemSpider ( 1 ) SID 46232210 - External ID: 137720 DiscoveryGate ( 1 ) SID 10252902 - External ID: 156391 ICCB-Longwood/NSRB Screening Facility, Harvard Medical School ( 3 ) SID 92124237 - External ID: HMS1920P13 SID 92308957 - External ID: HMS2089N21 SID 92307342 - External ID: HMS2091H12 LeadScope ( 1 ) SID 50025704 - External ID: LS-124738 NextBio ( 1 ) SID 50390002 - External ID: 156391 NIAID ( 1 ) SID 597410 - External ID: 001658 NINDS Approved Drug Screening Program ( 1 ) SID 8149438 - External ID: 01500425 NovoSeek ( 1 ) SID 57348284 - External ID: 156391 PDSP ( 1 ) SID 10321400 - External ID: Prestwick_349 xPharm ( 1 ) SID 7980083 - External ID: 9035
Chemical Reactions: 2 Links ChemSpider ( 1 ) SID 46232210 - External ID: 137720 ORST SMALL MOLECULE SCREENING CENTER ( 1 ) SID 26679674 - External ID: 01500425
Journal Publishers: 2 Links Thomson Pharma ( 2 ) SID 15172373 - External ID: 00001058 SID 15172374 - External ID: 00026895
NIH Molecular Libraries: Broad Institute ( 2 ) SID 85789204 - External ID: BRD-K59197931-001-02-9 SID 85789497 - External ID: BRD-K59197931-236-09-6 Sub. Code/Sub.Title: BI0409/ Chemoinformatics Laboratory Sem/Year: VII/IV
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Emory University Molecular Libraries Screening Center ( 1 ) SID 26611833 - External ID: SPECTRUM1500425 NCGC ( 3 ) SID 11112669 - External ID: NCGC00016759-01 SID 50103854 - External ID: NCGC00021127-01 SID 26755231 - External ID: NCGC00161591-01 SRMLSC ( 1 ) SID 46487915 - External ID: UPCMLD-DP001 The Scripps Research Institute Molecular Screening Center ( 1 ) SID 26527900 - External ID: SR-01000075977-3
Physical Properties: ChemExper Chemical Directory ( 1 ) SID 3248704 - External ID: jhiA`@@H|dwMkZ{IUgMT@@APPq`@ ChemSpider ( 1 ) SID 46232210 - External ID: 137720
Protein 3D Structures: 1 Link MMDB ( 1 ) SID 48426145 - External ID: 62694.9
Substance Vendors: 11 Links Ambinter ( 1 ) SID 25649496 - External ID: STOCK1N-50633 ChemExper Chemical Directory ( 1 ) SID 3248704 - External ID: jhiA`@@H|dwMkZ{IUgMT@@APPq`@ Hangzhou APIChem Technology ( 1 ) SID 92713624 - External ID: AC-1363 Hangzhou Trylead Chemical Technology ( 1 ) SID 49833549 - External ID: TL8003659 MolPort ( 1 ) SID 87623779 - External ID: MolPort-000-145-960 Sigma-Aldrich ( 5 ) TCI (Tokyo Chemical Industry) ( 1 ) SID 87572993 - External ID: M1021
Theoretical Properties: 1 Link ChemSpider ( 1 ) SID 46232210 - External ID: 137720
Toxicology: 2 Links ChemIDplus ( 1 ) SID 173087 - External ID: 022204531 EPA DSSTox ( 1 ) SID 56313690 - External ID: 48664
Canonical SMILES: CC(C1=CC2=C(C=C1)C=C(C=C2)OC)C(=O)O Sub. Code/Sub.Title: BI0409/ Chemoinformatics Laboratory Sem/Year: VII/IV
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InChI: InChI=1S/C14H14O3/c1-9(14(15)16)10-3-4-12-8-13(17-2)6-5-11(12)7-10/h3- 9H,1-2H3,(H,15,16)/t9-/m0/s1
SDF: 156391 -OEChem-07131002172D
31 32 0 1 0 0 0 0 0999 V2000 9.5312 1.5068 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5369 -0.5173 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4030 0.9827 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.2690 -0.5173 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 5.1350 -0.0173 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.8671 -0.0173 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.8671 0.9827 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0010 -0.5173 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1350 0.9827 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0010 1.4827 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2690 -1.5173 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7610 -0.5520 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7610 1.5173 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.6671 1.0035 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4030 -0.0173 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.6671 -0.0381 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.3991 1.0102 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8059 -0.8273 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 6.0010 -1.1373 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 4.5981 1.2927 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 6.0010 2.1027 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 3.6490 -1.5173 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2690 -2.1373 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 4.8890 -1.5173 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 7.7538 -1.1720 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 7.7538 2.1373 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 9.2028 -0.3502 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 2.0000 -0.2073 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 10.0912 0.4720 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 10.9372 0.7022 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 10.7070 1.5483 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 1 14 1 0 0 0 0 1 17 1 0 0 0 0 2 15 1 0 0 0 0 2 28 1 0 0 0 0 3 15 2 0 0 0 0 4 5 1 0 0 0 0 4 11 1 6 0 0 0 4 15 1 0 0 0 0 4 18 1 0 0 0 0 5 8 2 0 0 0 0 5 9 1 0 0 0 0 6 7 2 0 0 0 0 6 8 1 0 0 0 0 Sub. Code/Sub.Title: BI0409/ Chemoinformatics Laboratory Sem/Year: VII/IV
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6 12 1 0 0 0 0 7 10 1 0 0 0 0 7 13 1 0 0 0 0 8 19 1 0 0 0 0 9 10 2 0 0 0 0 9 20 1 0 0 0 0 10 21 1 0 0 0 0 11 22 1 0 0 0 0 11 23 1 0 0 0 0 11 24 1 0 0 0 0 12 16 2 0 0 0 0 12 25 1 0 0 0 0 13 14 2 0 0 0 0 13 26 1 0 0 0 0 14 16 1 0 0 0 0 16 27 1 0 0 0 0 17 29 1 0 0 0 0 17 30 1 0 0 0 0 17 31 1 0 0 0 0 M END $$$$
DICLOFENAC:
BioAssay Results:
Tested in BioAssays: All: 212 Active: 6 BioActivity Summary:
AID: 308403 Source: ChEMBL Displacement of fluorescent 5-Cyano-2-[(E)-2-(1-methyl-1H- indol-2-yl)-vinyl]-benzoic acid from human serum albumin
AID: 1811 Source: Shanghai Institute of Organic Chemistry Experimentally measured binding affinity data derived from PDB
AID: 1206 Source: NMMLSC Inhibitors of Bacterial Quorum Sensing: Summary
AID: 1195 Source: EPA DSSTox DSSTox (FDAMDD) FDA Maximum (Recommended) Daily Dose Database
Protein Structures: (Total: 9)
Sub. Code/Sub.Title: BI0409/ Chemoinformatics Laboratory Sem/Year: VII/IV
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MMDB ID: 78682 PDB ID: 2WEK Crystal Structure Of The Human Mgc45594 Gene Product In Complex With Diclofenac Taxonomy: Homo sapiens
MMDB ID: 75952 PDB ID: 3IB0 Structural Basis Of The Prevention Of Nsaid-Induced Damage Of The Gastrointestinal Tract By C-Terminal Half (C-Lobe) Of Bovine Colostrum Protein Lactoferrin: Binding And Structural Studies Of C-Lobe Complex With Diclofenac Taxonomy: Bos taurus MMDB ID: 69934 PDB ID: 3CFQ Crystal Structure Of Human Wild-Type Transthyretin In Complex With Diclofenac Taxonomy: Homo sapiens
Depositor-Supplied Synonyms: (Total: 102) diclofenac Diclofenac acid dichlofenac Diclofenacum Diclofenaco Diclophenac Pennsaid Dichlofenal Dicrofenac Novapirina
Properties Computed from Structure:
Molecular Weight 296.14864 [g/mol]
Molecular Formula C14H11Cl2NO2 XLogP3 4.4 H-Bond Donor 2 H-Bond Acceptor 3 Rotatable Bond Count 4 Exact Mass 295.016684 MonoIsotopic Mass 295.016684 Topological Polar Surface Area 49.3 Heavy Atom Count 19 Sub. Code/Sub.Title: BI0409/ Chemoinformatics Laboratory Sem/Year: VII/IV
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Formal Charge 0 Complexity 304 Isotope Atom Count 0 Defined Atom StereoCenter Count 0 Undefined Atom StereoCenter Count0 Defined Bond StereoCenter Count 0 Undefined Bond StereoCenter Count 0 Covalently-Bonded Unit Count 1
Descriptors Computed from Structure:
IUPAC Name: 2-[2-(2,6-dichloroanilino)phenyl]acetic acid Canonical SMILES: C1=CC=C(C(=C1)CC(=O)O)NC2=C(C=CC=C2Cl)Cl InChI: InChI=1S/C14H11Cl2NO2/c15-10-5-3-6-11(16)14(10)17-12-7-2-1-4-9(12)8-13 (18)19/h1-7,17H,8H2,(H,18,19) InChIKey: DCOPUUMXTXDBNB-UHFFFAOYSA-N
Compound Information:
CID 3033Create Date: 2005-03-25
Related Compounds: Same, Connectivity: 5 Links
Similar Compounds: 189 Links Similar Conformers: 237 Links View Conformers
Substance Information:
Substances: All: 479 Links Same structure: 77 Links Mixture: 402 Links
Category: [for same structure substances] Biological Properties: 52 Links BIDD ( 1 ) SID 93166538 - External ID: BIDD:GT0380 BindingDB ( 1 ) SID 46513484 - External ID: 13066 ChEBI ( 1 ) SID 29214789 - External ID: CHEBI:47381 ChemBank ( 37 ) ChemSpider ( 2 )
Sub. Code/Sub.Title: BI0409/ Chemoinformatics Laboratory Sem/Year: VII/IV
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SID 36519257 - External ID: 13852203 SID 29222179 - External ID: 2925 DiscoveryGate ( 1 ) SID 8151929 - External ID: 3033 DrugBank ( 1 ) SID 46504644 - External ID: DB00586 ICCB-Longwood/NSRB Screening Facility, Harvard Medical School ( 1 ) SID 92309046 - External ID: HMS2090C10 LeadScope ( 1 ) SID 49861545 - External ID: LS-11575 NextBio ( 1 ) SID 50910663 - External ID: 3033 NIAID ( 1 ) SID 641516 - External ID: 104206 NINDS Approved Drug Screening Program ( 1 ) SID 8149635 - External ID: 01500686 NovoSeek ( 1 ) SID 57321567 - External ID: 3033 Shanghai Institute of Organic Chemistry ( 1 ) SID 46393862 - External ID: 2b17 xPharm ( 1 ) SID 7979066 - External ID: 8288
Chemical Reactions: 2 Links ChemSpider ( 2 ) SID 36519257 - External ID: 13852203 SID 29222179 - External ID: 2925
Journal Publishers: 1 Link Thomson Pharma ( 1 ) SID 14873560 - External ID: 00011281
Metabolic Pathways: 2 Links KEGG ( 2 ) SID 4831 - External ID: C01690 SID 96024513 - External ID: D07816
NIH Molecular Libraries: 3 Links Broad Institute ( 1 ) SID 85787843 - External ID: BRD-K08252256-236-05-6 NCGC ( 1 ) SID 50103852 - External ID: NCGC00021125-01 NMMLSC ( 1 ) SID 24424557 - External ID: UNM000001216103
Physical Properties: 5 Links ChemSpider ( 2 ) SID 36519257 - External ID: 13852203 SID 29222179 - External ID: 2925 Sub. Code/Sub.Title: BI0409/ Chemoinformatics Laboratory Sem/Year: VII/IV
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DrugBank ( 1 ) SID 46504644 - External ID: DB00586 NIST ( 1 ) SID 10452425 - External ID: 492848439 NIST Chemistry WebBook ( 1 ) SID 10509002 - External ID: 492848439
Protein 3D Structures: 9 Links MMDB ( 8 ) SMID ( 1 ) SID 7887044 - External ID: DIF
Substance Vendors: 4 Links IS Chemical Technology ( 1 ) SID 93620648 - External ID: I14-7739 MolPort ( 1 ) SID 87360182 - External ID: MolPort-000-003-072 TCI (Tokyo Chemical Industry) ( 1 ) SID 87561265 - External ID: D3748 Tyger Scientific ( 1 ) SID 81049766 - External ID: D30801
Theoretical Properties: 4 Links ChemDB ( 1 ) SID 5394317 - External ID: 3966330 ChemSpider ( 2 ) SID 36519257 - External ID: 13852203 SID 29222179 - External ID: 2925 DrugBank ( 1 ) SID 46504644 - External ID: DB00586
Toxicology: 3 Links ChemIDplus ( 1 ) SID 169817 - External ID: 015307865 EPA DSSTox ( 2 ) SID 48415883 - External ID: 22923 SID 56313615 - External ID: 48589
Canonical SMILES: C1=CC=C(C(=C1)CC(=O)O)NC2=C(C=CC=C2Cl)Cl
InChI: InChI=1S/C14H11Cl2NO2/c15-10-5-3-6-11(16)14(10)17-12-7-2-1-4-9(12)8-13 (18)19/h1-7,17H,8H2,(H,18,19)
SDF:
3033 -OEChem-07131002202D Sub. Code/Sub.Title: BI0409/ Chemoinformatics Laboratory Sem/Year: VII/IV
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30 31 0 0 0 0 0 0 0999 V2000 2.0000 -1.5600 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 5.4641 -1.5600 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 4.5981 2.9400 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.8660 2.9400 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.7320 -0.5600 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 4.5981 0.9400 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5981 -0.0600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7320 1.4400 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7320 -1.5600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4641 1.4400 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4641 -0.5600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.3301 0.9400 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.3301 -0.0600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8660 -2.0600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5981 -2.0600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7320 2.4400 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8660 -3.0600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5981 -3.0600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7320 -3.5600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1215 1.5477 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5200 0.8574 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 3.1951 -0.2500 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 5.4641 2.0600 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 5.4641 -1.1800 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 6.8671 1.2500 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 6.8671 -0.3700 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 2.3291 -3.3700 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 5.1350 -3.3700 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 3.7320 -4.1800 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 4.5981 3.5600 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 1 14 1 0 0 0 0 2 15 1 0 0 0 0 3 16 1 0 0 0 0 3 30 1 0 0 0 0 4 16 2 0 0 0 0 5 7 1 0 0 0 0 5 9 1 0 0 0 0 5 22 1 0 0 0 0 6 7 1 0 0 0 0 6 8 1 0 0 0 0 6 10 2 0 0 0 0 7 11 2 0 0 0 0 8 16 1 0 0 0 0 8 20 1 0 0 0 0 8 21 1 0 0 0 0 9 14 2 0 0 0 0 9 15 1 0 0 0 0 10 12 1 0 0 0 0 10 23 1 0 0 0 0 11 13 1 0 0 0 0 11 24 1 0 0 0 0 12 13 2 0 0 0 0 Sub. Code/Sub.Title: BI0409/ Chemoinformatics Laboratory Sem/Year: VII/IV
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12 25 1 0 0 0 0 13 26 1 0 0 0 0 14 17 1 0 0 0 0 15 18 2 0 0 0 0 17 19 2 0 0 0 0 17 27 1 0 0 0 0 18 19 1 0 0 0 0 18 28 1 0 0 0 0 19 29 1 0 0 0 0 M END $$$$
KETOPROFEN:
BioAssay Results:
Tested in BioAssays: All: 153 Active: 1 Inactive: 133 BioActivity Summary:
AID: 1460 Source: NCGC qHTS for Inhibitors of Tau Fibril Formation, Thioflavin T Binding
AID: 449728 Source: The Scripps Research Institute Molecular Screening Center Counterscreen for inhibitors of AddAB: absorbance-based bacterial cell-based high throughput screening assay to identify inhibitors of bacterial viability
AID: 435030 Source: The Scripps Research Institute Molecular Screening Center Absorbance-based primary bacterial cell-based high throughput screening assay to identify inhibitors of AddAB recombination protein complex
AID: 435022 Source: Burnham Center for Chemical Genomics uHTS luminescence assay for the identification of chemical inhibitors of B-cell specific antigen receptor-induced NF-kB activation
Depositor-Supplied Synonyms: (Total: 34) ketoprofen (S)-Ketoprofen DEXKETOPROFEN (+)-Ketoprofen Dexketoprofen (INN) Dexketoprofen [INN] (S)-(+)-Ketoprofen BiomolKI_000007 BiomolKI2_000017 (+)-3-Benzoylhydratropic acid
Properties Computed from Structure: Sub. Code/Sub.Title: BI0409/ Chemoinformatics Laboratory Sem/Year: VII/IV
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Molecular Weight 254.28056 [g/mol]
Molecular Formula C16H14O3 XLogP3 3.1 H-Bond Donor 1 H-Bond Acceptor 3 Rotatable Bond Count 4 Exact Mass 254.094294 MonoIsotopic Mass 254.094294 Topological Polar Surface Area 54.4 Heavy Atom Count 19 Formal Charge 0 Complexity 331 Isotope Atom Count 0 Defined Atom StereoCenter Count 1 Undefined Atom StereoCenter Count0 Defined Bond StereoCenter Count 0 Undefined Bond StereoCenter Count 0 Covalently-Bonded Unit Count 1
Descriptors Computed from Structure:
IUPAC Name: (2S)-2-(3-benzoylphenyl)propanoic acid Canonical SMILES: CC(C1=CC=CC(=C1)C(=O)C2=CC=CC=C2)C(=O)O Isomeric SMILES: C[C@@H](C1=CC=CC(=C1)C(=O)C2=CC=CC=C2)C(=O)O InChI: InChI=1S/C16H14O3/c1-11(16(18)19)13-8-5-9-14(10-13)15(17)12-6-3-2-4-7- 12/h2-11H,1H3,(H,18,19)/t11-/m0/s1 InChIKey: DKYWVDODHFEZIM-NSHDSACASA-N
Compound Information:
CID 667550Create Date: 2005-07-07
Related Compounds: Same, Connectivity: 9 Links Same, Stereochemistry: 2 Links Same, Isotopes: 3 Links
Similar Compounds: 344 Links Similar Conformers: 43 Links View Conformers
Substance Information:
Sub. Code/Sub.Title: BI0409/ Chemoinformatics Laboratory Sem/Year: VII/IV
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Substances: All: 42 Links Same structure: 21 Links Mixture: 21 Links
Category: [for same structure substances] Biological Properties: 10 Links ChEBI ( 1 ) SID 85416182 - External ID: CHEBI:217758 ChemBank ( 2 ) SID 47885674 - External ID: BiomolKI_000007 SID 47589247 - External ID: BiomolKI2_000017 ChemSpider ( 1 ) SID 32961504 - External ID: 16736555 DiscoveryGate ( 1 ) SID 9276699 - External ID: 667550 ICCB-Longwood/NSRB Screening Facility, Harvard Medical School ( 1 ) SID 92309258 - External ID: HMS2090M22 LeadScope ( 1 ) SID 49878575 - External ID: LS-28622 NextBio ( 1 ) SID 50790838 - External ID: 667550 NovoSeek ( 1 ) SID 57408497 - External ID: 667550 xPharm ( 1 ) SID 7979052 - External ID: 8272
Chemical Reactions: 1 Link ChemSpider ( 1 ) SID 32961504 - External ID: 16736555
Journal Publishers: 1 Link Thomson Pharma ( 1 ) SID 14774446 - External ID: 00011946
Metabolic Pathways: 1 Link KEGG ( 1 ) SID 51091607 - External ID: D07269
NIH Molecular Libraries: 2 Links NCGC ( 2 ) SID 26754382 - External ID: NCGC00142585-01 SID 26754383 - External ID: NCGC00142585-02
NIH Substance Repository: 2 Links MLSMR ( 2 ) SID 56320639 - External ID: MLS001333189 SID 56320640 - External ID: MLS001333190
Sub. Code/Sub.Title: BI0409/ Chemoinformatics Laboratory Sem/Year: VII/IV
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Physical Properties: 1 Link ChemSpider ( 1 ) SID 32961504 - External ID: 16736555
Substance Vendors: 4 Links Ambinter ( 1 ) SID 48491693 - External ID: ST066909 MolPort ( 1 ) SID 89386915 - External ID: MolPort-002-343-983 Sigma-Aldrich ( 2 ) SID 24870770 - External ID: 471909_ALDRICH SID 24896218 - External ID: K2135_SIGMA
Theoretical Properties: 1 Link ChemSpider ( 1 ) SID 32961504 - External ID: 16736555
Toxicology: 1 Link ChemIDplus ( 1 ) SID 173013 - External ID: 022161815
Canonical SMILES: CC(C1=CC=CC(=C1)C(=O)C2=CC=CC=C2)C(=O)O
InChI: InChI=1S/C16H14O3/c1-11(16(18)19)13-8-5-9-14(10-13)15(17)12-6-3-2-4-7- 12/h2-11H,1H3,(H,18,19)
SDF: 3825 -OEChem-07131002222D
33 34 0 1 0 0 0 0 0999 V2000 2.0000 -2.9400 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.7320 2.0600 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.7320 -2.9400 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.8660 -1.4400 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 3.7320 -0.9400 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7320 0.0600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5981 0.5600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5981 -1.4400 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0000 -0.9400 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4641 0.0600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4641 -0.9400 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5981 1.5600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8660 -2.4400 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4641 2.0600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4641 3.0600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.3301 1.5600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
Sub. Code/Sub.Title: BI0409/ Chemoinformatics Laboratory Sem/Year: VII/IV
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6.3301 3.5600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.1962 2.0600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.1962 3.0600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1299 -1.8650 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 3.1951 0.3700 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 4.5981 -2.0600 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 2.3100 -0.4031 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4631 -0.6300 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6900 -1.4769 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 6.0010 0.3700 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 6.0010 -1.2500 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 4.9272 3.3700 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 6.3301 0.9400 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 6.3301 4.1800 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 7.7331 1.7500 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 7.7331 3.3700 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 2.0000 -3.5600 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 1 13 1 0 0 0 0 1 33 1 0 0 0 0 2 12 2 0 0 0 0 3 13 2 0 0 0 0 4 5 1 0 0 0 0 4 9 1 0 0 0 0 4 13 1 0 0 0 0 4 20 1 0 0 0 0 5 6 1 0 0 0 0 5 8 2 0 0 0 0 6 7 2 0 0 0 0 6 21 1 0 0 0 0 7 10 1 0 0 0 0 7 12 1 0 0 0 0 8 11 1 0 0 0 0 8 22 1 0 0 0 0 9 23 1 0 0 0 0 9 24 1 0 0 0 0 9 25 1 0 0 0 0 10 11 2 0 0 0 0 10 26 1 0 0 0 0 11 27 1 0 0 0 0 12 14 1 0 0 0 0 14 15 2 0 0 0 0 14 16 1 0 0 0 0 15 17 1 0 0 0 0 15 28 1 0 0 0 0 16 18 2 0 0 0 0 16 29 1 0 0 0 0 17 19 2 0 0 0 0 17 30 1 0 0 0 0 18 19 1 0 0 0 0 18 31 1 0 0 0 0 19 32 1 0 0 0 0 M END $$$$
Sub. Code/Sub.Title: BI0409/ Chemoinformatics Laboratory Sem/Year: VII/IV
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ASPIRIN: BioAssay Results:
Tested in BioAssays: All: 1052 Active: 11 Inactive: 393 BioActivity Summary:
AID: 421503 Source: ChEMBL Antioxidant activity in Sprague-Dawley rat brain homogenate assessed as attenuation of toxin- induced lipid peroxidation at 1 mM by modified TBA assay
AID: 338339 Source: ChEMBL Antiplatelet activity against rat platelet rich plasma assessed as inhibition of ADP-induced platelet aggregation at 1 mg/ml pretreated 2 mins before ADP challenge
AID: 338337 Source: ChEMBL Antiplatelet activity against rat platelet rich plasma assessed as inhibition of arachidonic acid- induced platelet aggregation at 0.1 mg/ml pretreated 2 mins before arachidonic acid challenge
AID: 338336 Source: ChEMBL Antiplatelet activity against rat platelet rich plasma assessed as inhibition of collagen-induced platelet aggregation at 0.25 mg/ml pretreated 2 mins before collagen challenge more ...
Protein Structures: (Total: 5)
MMDB ID: 75951 PDB ID: 3IAZ Structural Basis Of The Prevention Of Nsaid-Induced Damage Of The Gastrointestinal Tract By C-Terminal Half (C-Lobe) Of Bovine Colostrum Protein Lactoferrin: Binding And Structural Studies Of The C-Lobe Complex With Aspirin Taxonomy: Bos taurus MMDB ID: 70578 PDB ID: 3GCL Mode Of Ligand Binding And Assignment Of Subsites In Mammalian Peroxidases: Crystal Structure Of Lactoperoxidase Complexes With Acetyl Salycylic Acid, Salicylhydroxamic Acid And Benzylhydroxamic Acid Taxonomy: Bos taurus
MMDB ID: 54234 PDB ID: 2QQT Crystal Structure Of The Complex Of Bovine Lactoperoxidase With Acetyl Salicylic Acid At 2.5 A Resolution Taxonomy: Bos taurus
Sub. Code/Sub.Title: BI0409/ Chemoinformatics Laboratory Sem/Year: VII/IV
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Depositor-Supplied Synonyms: (Total: 346) aspirin ACETYLSALICYLIC ACID Acylpyrin Colfarit Ecotrin Enterosarein Acenterine Polopiryna Micristin Acetosal
Properties Computed from Structure:
Molecular Weight 180.15742 [g/mol]
Molecular Formula C9H8O4 XLogP3 1.2 H-Bond Donor 1 H-Bond Acceptor 4 Rotatable Bond Count 3 Exact Mass 180.042259 MonoIsotopic Mass 180.042259 Topological Polar Surface Area 63.6 Heavy Atom Count 13 Formal Charge 0 Complexity 212 Isotope Atom Count 0 Defined Atom StereoCenter Count 0 Undefined Atom StereoCenter Count0 Defined Bond StereoCenter Count 0 Undefined Bond StereoCenter Count 0 Covalently-Bonded Unit Count 1
Descriptors Computed from Structure:
IUPAC Name: 2-acetyloxybenzoic acid Canonical SMILES: CC(=O)OC1=CC=CC=C1C(=O)O InChI: InChI=1S/C9H8O4/c1-6(10)13-8-5-3-2-4-7(8)9(11)12/h2-5H,1H3,(H,11,12) InChIKey: BSYNRYMUTXBXSQ-UHFFFAOYSA-N
Compound Information:
Sub. Code/Sub.Title: BI0409/ Chemoinformatics Laboratory Sem/Year: VII/IV
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CID 2244 Create Date: 2004-09-16
Related Compounds: Same, Connectivity: 3 Links
Similar Compounds: 1636 Links Similar Conformers: 828 Links View Conformers
Substance Information:
Substances: All: 871 Links Same structure: 129 Links Mixture: 742 Links
Category: [for same structure substances] Biological Properties: 76 Links BIDD ( 1 ) SID 93166276 - External ID: BIDD:GT0118 BindingDB ( 1 ) SID 49846175 - External ID: 22360 ChEBI ( 1 ) SID 8143164 - External ID: CHEBI:15365 ChemBank ( 25 ) ChemSpider ( 32 ) Circadian Research, Kay Laboratory, University of California at San Diego (UCSD) ( 1 ) SID 92303504 - External ID: A 5376 Comparative Toxicogenomics Database ( 1 ) SID 53788943 - External ID: D001241 DiscoveryGate ( 1 ) SID 8151516 - External ID: 2244 DrugBank ( 1 ) SID 46505803 - External ID: DB00945 DTP/NCI ( 2 ) SID 87798 - External ID: 27223 SID 476106 - External ID: 406186 ICCB-Longwood/NSRB Screening Facility, Harvard Medical School ( 3 ) SID 92124017 - External ID: HMS1920E13 SID 92309119 - External ID: HMS2090G03 SID 92307403 - External ID: HMS2091K13 LeadScope ( 1 ) SID 49854366 - External ID: LS-143 NextBio ( 1 ) SID 50796606 - External ID: 2244 NIAID ( 1 ) SID 602429 - External ID: 006788 NINDS Approved Drug Screening Program ( 1 ) Sub. Code/Sub.Title: BI0409/ Chemoinformatics Laboratory Sem/Year: VII/IV
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SID 8149208 - External ID: 01500130 NovoSeek ( 1 ) SID 57321220 - External ID: 2244 Shanghai Institute of Organic Chemistry ( 1 ) SID 46392828 - External ID: 1oxr xPharm ( 1 ) SID 7978731 - External ID: 7904
Chemical Reactions: 34 Links ChemSpider ( 32 ) Comparative Toxicogenomics Database ( 1 ) SID 53788943 - External ID: D001241 ORST SMALL MOLECULE SCREENING CENTER ( 1 ) SID 26679412 - External ID: 00211363
Journal Publishers: 2 Links Prous Science Drugs of the Future ( 1 ) SID 24714725 - External ID: 91341 Thomson Pharma ( 1 ) SID 15195166 - External ID: 00002661
Metabolic Pathways: 4 Links Comparative Toxicogenomics Database ( 1 ) SID 53788943 - External ID: D001241 Golm Metabolome Database (GMD), Max Planck Institute of Molecular Plant Physiology ( 1 ) SID 92297672 - External ID: D41527A7-A9EB-472D-A7FC-312821130549 KEGG ( 2 ) SID 4594 - External ID: C01405 SID 7847177 - External ID: D00109
NIH Molecular Libraries: 14 Links Emory University Molecular Libraries Screening Center ( 2 ) SID 17404602 - External ID: EU-0100038 SID 26611613 - External ID: SPECTRUM1500130 NCGC ( 10 ) NMMLSC ( 1 ) SID 81067407 - External ID: UNM-0000306102 University of Pittsburgh Molecular Library Screening Center ( 1 ) SID 53777144 - External ID: 659
NIH Substance Repository: 4 Links MLSMR ( 4 ) SID 49826121 - External ID: MLS001055329 SID 47193676 - External ID: MLS001066332 SID 57260466 - External ID: MLS001336045 SID 57260467 - External ID: MLS001336046
Physical Properties: 38 Links ChemExper Chemical Directory ( 1 ) Sub. Code/Sub.Title: BI0409/ Chemoinformatics Laboratory Sem/Year: VII/IV
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SID 3135921 - External ID: HklB@@QmR[fUxUZBBF@@@ ChemSpider ( 32 ) DrugBank ( 1 ) SID 46505803 - External ID: DB00945 MP Biomedicals ( 1 ) SID 85083307 - External ID: 150245 NIST ( 1 ) SID 10396336 - External ID: 2512372342 NIST Chemistry WebBook ( 1 ) SID 10524572 - External ID: 2512372342 NMRShiftDB ( 1 ) SID 840714 - External ID: 20038075
Protein 3D Structures: 6 Links MMDB ( 5 ) SMID ( 1 ) SID 7885805 - External ID: AIN
Substance Vendors: 10 Links Ambinter ( 1 ) SID 94514523 - External ID: Ambku20129 ChemExper Chemical Directory ( 1 ) SID 3135921 - External ID: HklB@@QmR[fUxUZBBF@@@ IS Chemical Technology ( 1 ) SID 93620436 - External ID: I14-7505 MolPort ( 1 ) SID 88519611 - External ID: MolPort-000-871-622 MP Biomedicals ( 1 ) SID 85083307 - External ID: 150245 Sigma-Aldrich ( 4 ) SID 24890623 - External ID: A2093_SIGMA SID 24890723 - External ID: A3160_SIGMA SID 24278218 - External ID: A5376_SIGMA SID 24891140 - External ID: A6810_SIGMA TCI (Tokyo Chemical Industry) ( 1 ) SID 87561583 - External ID: A2262
Theoretical Properties: 34 Links ChemDB ( 1 ) SID 5261264 - External ID: 3965510 ChemSpider ( 32 ) DrugBank ( 1 ) SID 46505803 - External ID: DB00945
Toxicology: 10 Links ChemIDplus ( 1 ) SID 148573 - External ID: 000050782 Comparative Toxicogenomics Database ( 1 ) SID 53788943 - External ID: D001241 Sub. Code/Sub.Title: BI0409/ Chemoinformatics Laboratory Sem/Year: VII/IV
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EPA DSSTox ( 8 )
Canonical SMILES: CC(=O)OC1=CC=CC=C1C(=O)O
InChI: InChI=1S/C9H8O4/c1-6(10)13-8-5-3-2-4-7(8)9(11)12/h2-5H,1H3,(H,11,12)
SDF:
2244 -OEChem-07131002242D
21 21 0 0 0 0 0 0 0999 V2000 3.7320 -0.0600 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.3301 1.4400 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.5981 1.4400 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.8660 -1.5600 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.5981 -0.5600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4641 -0.0600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5981 -1.5600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.3301 -0.5600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4641 -2.0600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.3301 -1.5600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4641 0.9400 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8660 -0.5600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0000 -0.0600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0611 -1.8700 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 6.8671 -0.2500 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 5.4641 -2.6800 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 6.8671 -1.8700 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 2.3100 0.4769 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4631 0.2500 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6900 -0.5969 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 6.3301 2.0600 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 1 5 1 0 0 0 0 1 12 1 0 0 0 0 2 11 1 0 0 0 0 2 21 1 0 0 0 0 3 11 2 0 0 0 0 4 12 2 0 0 0 0 5 6 1 0 0 0 0 5 7 2 0 0 0 0 6 8 2 0 0 0 0 6 11 1 0 0 0 0 7 9 1 0 0 0 0 7 14 1 0 0 0 0 8 10 1 0 0 0 0 8 15 1 0 0 0 0 9 10 2 0 0 0 0 Sub. Code/Sub.Title: BI0409/ Chemoinformatics Laboratory Sem/Year: VII/IV
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9 16 1 0 0 0 0 10 17 1 0 0 0 0 12 13 1 0 0 0 0 13 18 1 0 0 0 0 13 19 1 0 0 0 0 13 20 1 0 0 0 0 M END $$$$
THE CHEMICAL FILE FORMATS AVAILABLE IN ZINC FOR THE ABOVE CHEMICAL COMPOUNDS ARE:
TOLMETIN: NA
NAPROXEN:NA
DICLOFENAC:NA
KETOPROFEN:NA
ASPIRIN:NA
THE CHEMICAL FILE FORMATS AVAILABLE IN CHEMEXPER FOR THE ABOVE CHEMICAL COMPOUNDS ARE:
TOLMETIN:
MOL:
19 20 0 0 0 0 0 0 0 0999 V2000 5.0820 2.2205 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.0874 2.1159 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4997 2.9249 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6807 1.2024 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9064 3.8385 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5051 2.8204 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7026 0.9945 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 4.1807 0.3364 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3186 4.6475 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9173 3.6294 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5980 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9594 1.6636 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5116 -0.4067 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3241 4.5430 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7320 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7363 5.3520 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
Sub. Code/Sub.Title: BI0409/ Chemoinformatics Laboratory Sem/Year: VII/IV
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0.8660 1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 0 0 0 2 3 1 0 0 0 0 2 4 1 0 0 0 0 3 5 2 0 0 0 0 3 6 1 0 0 0 0 4 7 1 0 0 0 0 4 8 2 0 0 0 0 5 9 1 0 0 0 0 6 10 2 0 0 0 0 7 11 1 0 0 0 0 7 12 1 0 0 0 0 8 13 1 0 0 0 0 9 14 2 0 0 0 0 11 15 1 0 0 0 0 14 16 1 0 0 0 0 15 17 1 0 0 0 0 17 18 2 0 0 0 0 17 19 1 0 0 0 0 10 14 1 0 0 0 0 11 13 2 0 0 0 0 M END
NAPROXEN:
Canonical SMILES: N(C1(=C(Cl)C=CC=C1Cl))C=2(C(CC(=O)O)=CC=CC=2)
1S/C14H11Cl2NO2/c15-10-5-3-6-11(16)14(10)17-12-7-2-1-4-9(12)8-13(18)19/h1- InChI: 7,17H,8H2,(H,18,19)
MOL: 19 20 0 0 0 0 0 0 0 0999 V2000 1.7320 1.4999 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1.7320 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5980 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5980 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5980 2.9999 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7320 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 2.4999 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 2.4999 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7320 4.4999 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 1.4999 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5980 3.9999 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 3.9999 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 Sub. Code/Sub.Title: BI0409/ Chemoinformatics Laboratory Sem/Year: VII/IV
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4.3301 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 0 0 0 0 3 1 1 0 0 0 0 4 3 1 0 0 0 0 5 8 1 0 0 0 0 6 2 2 0 0 0 0 7 2 1 0 0 0 0 8 4 1 0 0 0 0 9 5 2 0 0 0 0 10 6 1 0 0 0 0 11 7 1 0 0 0 0 12 5 1 0 0 0 0 13 16 1 0 0 0 0 14 3 2 0 0 0 0 15 6 1 0 0 0 0 16 7 2 0 0 0 0 17 4 2 0 0 0 0 18 14 1 0 0 0 0 19 18 2 0 0 0 0 13 15 2 0 0 0 0 19 17 1 0 0 0 0 M END
DICLOFENAC:
1S/C14H11Cl2NO2/c15-10-5-3-6-11(16)14(10)17-12-7-2-1-4-9(12)8-13(18)19/h1- InChI: 7,17H,8H2,(H,18,19) Canonical Smiles: N(C1(=C(Cl)C=CC=C1Cl))C=2(C(CC(=O)O)=CC=CC=2)
MOL:
19 20 0 0 0 0 0 0 0 0999 V2000 1.7320 1.4999 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1.7320 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5980 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5980 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5980 2.9999 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7320 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 2.4999 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 2.4999 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7320 4.4999 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 1.4999 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5980 3.9999 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 3.9999 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 Sub. Code/Sub.Title: BI0409/ Chemoinformatics Laboratory Sem/Year: VII/IV
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4.3301 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 0 0 0 0 3 1 1 0 0 0 0 4 3 1 0 0 0 0 5 8 1 0 0 0 0 6 2 2 0 0 0 0 7 2 1 0 0 0 0 8 4 1 0 0 0 0 9 5 2 0 0 0 0 10 6 1 0 0 0 0 11 7 1 0 0 0 0 12 5 1 0 0 0 0 13 16 1 0 0 0 0 14 3 2 0 0 0 0 15 6 1 0 0 0 0 16 7 2 0 0 0 0 17 4 2 0 0 0 0 18 14 1 0 0 0 0 19 18 2 0 0 0 0 13 15 2 0 0 0 0 19 17 1 0 0 0 0 M END
KETOPROFEN:
1S/C16H14O3/c1-11(16(18)19)13-8-5-9-14(10-13)15(17)12-6-3-2-4-7-12/h2- InChI: 11H,1H3,(H,18,19) Canonical SMILES: C(C=1(C=C(C(C(=O)O)C)C=CC=1))(=O)C2(=CC=CC=C2)
MOL:
19 20 0 0 0 0 0 0 0 0999 V2000 3.4641 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5980 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5980 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7320 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5980 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -0.4999 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7320 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5980 4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7320 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 Sub. Code/Sub.Title: BI0409/ Chemoinformatics Laboratory Sem/Year: VII/IV
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1.7320 4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 0 0 0 0 3 6 1 0 0 0 0 4 5 2 0 0 0 0 5 2 1 0 0 0 0 6 4 1 0 0 0 0 7 1 2 0 0 0 0 8 3 2 0 0 0 0 9 1 1 0 0 0 0 10 3 1 0 0 0 0 11 2 2 0 0 0 0 12 13 2 0 0 0 0 13 11 1 0 0 0 0 14 6 1 0 0 0 0 15 9 2 0 0 0 0 16 9 1 0 0 0 0 17 15 1 0 0 0 0 18 16 2 0 0 0 0 19 18 1 0 0 0 0 17 19 2 0 0 0 0 4 12 1 0 0 0 0 M END
ASPIRIN:
InChI: 1S/C9H8O4/c1-6(10)13-8-5-3-2-4-7(8)9(11)12/h2-5H,1H3,(H,11,12) Canonical SMILES: C1(C(=O)O)(=C(OC(=O)C)C=CC=C1)
MOL:
13 13 0 0 0 0 0 0 0 0999 V2000 2.5980 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7320 1.4999 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5980 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7320 -0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7320 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7320 2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5980 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 1.4999 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 0 0 0 0 3 1 2 0 0 0 0 4 3 1 0 0 0 0 Sub. Code/Sub.Title: BI0409/ Chemoinformatics Laboratory Sem/Year: VII/IV
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5 4 1 0 0 0 0 6 2 2 0 0 0 0 7 5 2 0 0 0 0 8 2 1 0 0 0 0 9 1 1 0 0 0 0 10 3 1 0 0 0 0 11 5 1 0 0 0 0 12 9 2 0 0 0 0 13 12 1 0 0 0 0 13 10 2 0 0 0 0 M END
THE CHEMICAL FILE FORMATS AVAILABLE IN CHEMBANK FOR THE ABOVE CHEMICAL COMPOUNDS ARE:
TOLMETIN:
SMILES:Cc1ccc(cc1) C(=O) c2ccc(CC(=O) O) n2C
InChI: 1/C15H15NO3/c1- 10- 3- 5- 11(6- 4- 10) 15(19) 13- 8- 7- 12(16(13) 2) 9- 14(17) 18/h3- 8H,9H2,1- 2H3,(H,17,18)
NAPROXEN:
SMILES:COc1ccc2cc(ccc2c1) [C@@H](C) C(=O) O
1/C14H14O3/c1- 9(14(15) 16) 10- 3- 4- 12- 8- 13(17- 2) 6- 5- 11(12) 7- 10/h3- 9H,1- InChI: 2H3,(H,15,16)
DICLOFENAC:
SMILES:OC(=O) Cc1ccccc1Nc2c(Cl) cccc2Cl
1/C14H11Cl2NO2/c15- 10- 5- 3- 6- 11(16) 14(10) 17- 12- 7- 2- 1- 4- 9(12) 8- 13(18) InChI: 19/h1- 7,17H,8H2,(H,18,19)
KETOPROFEN:
SMILES:CC(C(=O) O) c1cccc(c1) C(=O) c2ccccc2 1/C16H14O3/c1- 11(16(18) 19) 13- 8- 5- 9- 14(10- 13) 15(17) 12- 6- 3- 2- 4- 7- 12/h2- 11H,1H3,(H,18,19)
InChI:
Sub. Code/Sub.Title: BI0409/ Chemoinformatics Laboratory Sem/Year: VII/IV
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ASPIRIN:
SMILES:CC(=O) Oc1ccccc1C(=O) O
InChI: 1/C9H8O4/c1- 6(10) 13- 8- 5- 3- 2- 4- 7(8) 9(11) 12/h2- 5H,1H3,(H,11,12)
THE CHEMICAL FILE FORMATS AVAILABLE IN PDBEBANK FOR THE ABOVE CHEMICAL COMPOUNDS ARE:
TOLMETIN: No results.
NAPROXEN: No results.
DICLOFENAC: No results.
KETOPROFEN: No results.
ASPIRIN: No results.
Result: The task assigned has been executed successfully. Ex no:4 Date:
Chemoinformatics Queries
Aim: To get the ways & results to perform the given queries. Sub. Code/Sub.Title: BI0409/ Chemoinformatics Laboratory Sem/Year: VII/IV
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1. a. How do you do virtual screening for this compound?
A-1.a.Ways: 1.Virtual screening can be performed by using the ZINC:- i.Draw the structure & click Run Query. ii. On Clicking the Run Query we get the list of compounds containing the above structure
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iii.We also get a SMILE format: CC(=O)Oc1ccccc1C(=O)O
With the help of smile format we cam go to PubChem to get the following information:
1. b. How many H- Bond Donor and acceptor are there?
A-1.b.There is 1 hydrogen bond donor and 4 hydrogen bond acceptor.
1. c. What are the Pharmacological actions?
A-1.c.Anti-Inflammatory Agents, Non-Steroidal - Anti-inflammatory agents that are not steroids. In addition to anti-inflammatory actions, they have analgesic, antipyretic,etc.
Fibrinolytic Agents - Fibrinolysin or agents that convert plasminogen to fibrinolysin (PLASMIN). Platelet Aggregation Inhibitors - Drugs or agents which antagonize or impair any mechanism leading to blood platelet aggregation, whether during the phases of Sub. Code/Sub.Title: BI0409/ Chemoinformatics Laboratory Sem/Year: VII/IV
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activation etc.
Cyclooxygenase Inhibitors - Compounds or agents that combine with cyclooxygenase (PROSTAGLANDIN-ENDOPEROXIDE SYNTHASES) and thereby prevent its substrate-enzyme etc.
1. d. How many active and inactive Bioassays are there?
A-1.d.Active: 11 Inactive: 393
1. e. How many similar compounds are found?
A-1.e.There are 18 similar molecules found.
2. How to search a compound with lipanski violation: 3
A-2Way: This search can be performed using ChemBank: by descriptor.
Result: Total 12193 compounds.
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3. What is the drug produced by fisher. A-3Way:Result obtained from ChemBank: Search by Chemist.
Result:1 Molecule Found.
4. How many compounds are newly added in the chemical database for this month? A-4.Results obtained by using limits in the PubChem: Sub. Code/Sub.Title: BI0409/ Chemoinformatics Laboratory Sem/Year: VII/IV
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Total 260 compounds between 2010/06/27 to 2010/07/27.
5. How many compounds are there with rhenium (Re)? A-5.a.2 methods are there either use limits that gives no results:
b.Search directly in PubChem compounds:
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6. How many phenol compounds are there with Fully unspecified chiral centers, Partially specified chiral centers, Fully specified chiral centers A-6.Way:Results obtained by using limits in the PubChem: Fully unspecified chiral centers:
Result:25303 compounds. Partially specified chiral centers:
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Result:753 compounds. Fully specified chiral centers:
Result:16403 compounds.
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7. How many compounds are found with CovalentUnitCount from 5 to 10?
A-7.Way:Results obtained by using limits in the PubChem: Result:141382 compounds.
8. How many exact and how many substructures are available for the following structure?
A-8.Way: 1.First use zinc for the screening of the compound: Exact:
Substructure:-more than 100 Sub. Code/Sub.Title: BI0409/ Chemoinformatics Laboratory Sem/Year: VII/IV
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2.Smiles were Oc2ccc(OCc1ccccc1)cc2 were obtained. 3.Then use ChemBank for the search: Exact:2 molecules found.
Substructure: 1203 molecules found.
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Result:The results for the given queries were obtained. Ex no:5 Date:
Chemoinformatics Queries
Download 3B92.pdb for the following experiments
RASMOL URL: http://rasmol.org/
RasMol is a program for molecular graphics visualisation originally developed by Roger Sayle. This site is provided for the convenience of users of RasMol and developers of open source versions of RasMol. The site itself is provided courtesy of Bernstein + Sons. Maintenance of RasMol, much of the development, and integration of modifications provided by the community is done at the ARCiB laboratory at Dowling College. For the convenience of contributors to the RasMol project, two open source collaborative development sites are used:
• http://blondie.dowling.edu/projects/rasmol is the internal development GFORGE site in the ARCiB laboratory at Dowling College
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• http://www.sourceforge.net/projects/openrasmol is the external development site provided by SourceForge, Inc.
Members of the community are welcome to join us on either or both sites. The http://blondie.dowling.edu/projects/rasmol provides a more intimate view of development work in progress. The sourceforge site has fewer development threads, and is therefore more stable.
Work on RasMol has been supported in part by grants from the U.S. Department of Energy, the U.S. National Science Foundation and the U.S. NIH National Institute of General Medical Sciences. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the funding agencies.
Start RasMol and open 3B92.pdb in RasMol. Perform the following
1. Change the background color to white.
2. Display protein in ribbon format and ligand in spacefill format.
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3. Display and label the ligand(s) in relation to the protein.
4. How many histidine residues are present? Show them in red colored spacefill format.
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5. How many helices are there? Show them in magenta colored ribbon format.
6. How many sheets are there? Show them in blue colored ribbon format.
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7. Select glutamic acid at 308th position. Show it in space fill format- color by cpk.
8. Show the hydrophobic and polar residues in spacefill format. Color them with blue and red respectively.
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9. Show the charged residues in spacefill format. Pick and write on the any five residues.
10. Save the file in gif format. A.10.Export to gif.
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CHIMERA
URL: http://www.cgl.ucsf.edu/chimera/
UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality images and animations can be generated. Chimera includes complete documentation and several tutorials, and can be downloaded free of charge for academic, government, non-profit, and personal use. Chimera is developed by the Resource for Biocomputing, Visualization, and Informatics and funded by the NIH National Center for Research Resources (grant P41-RR01081).
1. To find out specific aminoacid like – eg: select specific histidine
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2. Show the surface view or ribbons etc
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3. Match maker – to find the identity or RMSD value
4. How to minimize the structure
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5. File saving formats
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6. Select the ligand
7. Select the HOH
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PYMOL URL: http://www.pymol.org/
PyMOL is Good for:
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1. Viewing 3D Molecular Structures 2. Rendering Figures Artistically 3. Animating Molecules Dynamically 4. Giving Live 3D Presentations 5. Sharing Interactive Visualizations 6. Exporting Geometry: VRML, OBJ, …
1. To find the Active Site Residues
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Result: The results for the given queries were obtained.
Ex no:6 Date:
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Queries based on chemical Sketching tools
ChemSketch:
URL: http://www.acdlabs.com/resources/freeware/chemsketch/
ACD/ChemSketch Freeware is a drawing package that allows you to draw chemical structures including organics, organometallics, polymers, and Markush structures. It also includes features such as calculation of molecular properties (e.g., molecular weight, density, molar refractivity etc.), 2D and 3D structure cleaning and viewing, functionality for naming structures (fewer than 50 atoms and 3 rings), and prediction of logP
1. Draw the following structure and answer the questions using CHEMSKETCH.
A. Name of the structure.
5,5-diphenylimidazolidine-2,4-dione
B. SMILES notation.
O=C2NC(=O)NC2(c1ccccc1)c3ccccc3
C. Molar refractivity.
Molar Refractivity = 69.58 ± 0.3 cm3
D. Surface tension.
Surface Tension = 49.2 ± 3.0 dyne/cm
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2. Draw the structure of 1, 2 dicholoroethylene and answer the questions using CHEMSKETCH. A. Trans and cis forms.
B. Show stereo descriptors for both. Sub. Code/Sub.Title: BI0409/ Chemoinformatics Laboratory Sem/Year: VII/IV
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C. InChI format. InChI=1/2C2H2Cl2/c2*3‐1‐2‐4/h2*1‐2H/b2*2‐1+
D. Create 3D structure.
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3. Draw the following structure and answer the questions using CHEMSKETCH.
A. Name of the structure.
3-ethyl-3-methylpyrrolidine-2,5-dione
B. Polarizability
Polarizability = 14.26 ± 0.5 10-24cm3
C. Dielectric constant
Dielectric Constant = Not available
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Index of Refraction = 1.450 ± 0.02
4. Draw the following structure and answer the questions using CHEMSKETCH.
A. Name of the structure.
N-(4-hydroxyphenyl)acetamide
B. SMILES notation.
Oc1ccc(NC(C)=O)cc1
C. Use of the compound
anti-pyretic ,analgesic
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D. Number of aromatics groups. One
5. Draw the structure of 2, 4 dinitrophenol and answer the questions using CHEMSKETCH. A. Any five important properties. Molecular Weight 184.10636 [g/mol]
Molecular Formula C6H4N2O5 XLogP3 1.7 H-Bond Donor 1 H-Bond Acceptor 5
B. SMILES notation.
O=[N+]([O-])c1cc(ccc1O)[N+]([O-])=O
C. Create 3D structure.
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D. Save and display the mol format
6. Create the 3D structure of the following using CHEMSKETCH.
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Result: The results for the given queries were obtained.
Ex no:7 Date: Queries based on chemical Sketching tools
ISIS Draw: 1. Now available as Symyx Draw. 2. It is a chemical structure drawing program for windows, published by MDL information system.
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Result: The results for the given queries were obtained.
Ex no:8 Date: Sub. Code/Sub.Title: BI0409/ Chemoinformatics Laboratory Sem/Year: VII/IV
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Molecular Property Calculation using Osiris
Aim: To calculate molecular properties using Osiris.
Procedure:
URL: http://www.organic-chemistry.org/prog/peo
Osiris: 1. It let us draw chemical structures and calculates on the fly various drug relevant properties whenever a structure is valid. 2. Prediction values are valued and color coded. 3. Properties like high risks of undesired effects like mutagenicity or a poor intestinal absorption are shown in red. 4. Whereas Green color indicates drug-conform behavior.
Benzene
Phenol
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Chloro Benzene
2-Chloro Phenol
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2-Chloro-4-sulfanylphenol
Observation:
Compound ClogP Solubility Molweight Druglikeness Drug- Sub. Code/Sub.Title: BI0409/ Chemoinformatics Laboratory Sem/Year: VII/IV
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Score Benzene 1.98 -1.62 78.0 -4.84 0.06 Phenol 1.68 -1.32 94.0 -2.3 0.07 Chloro 2.6 -2.35 112 -2.17 0.11 Benzene 2-Chloro 2.3 -2.06 128 -1.47 0.12 Phenol 2-Chloro-4- 2.48 -3.16 160 -3.4 0.46 sulfanylphenol
Result: The molecular properties for the desired compounds calculated. Ex no:9 Date: Chemical Database Creation using Chimera
Aim: To create a chemical database using UCSF Chimera.
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URL: http://www.cgl.ucsf.edu/chimera
UCSF Chimera:
UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality images and animations can be generated. Chimera includes complete documentation and several tutorials, and can be downloaded free of charge for academic, government, non-profit, and personal use. Chimera is developed by the Resource for Biocomputing, Visualization, and Informatics and funded by the NIH National Center for Research Resources
Steps involved:
1. Download 20 compounds with similar therapeutic properties e.g. Anti- cancer,anti-tuberculosis etc. in sdf format. 2. Open chimera 3. Open all the saved molecules of sdf format. 4. ToolsÆstructure editingÆminimise structureÆclick minimiseÆcheck all the boxes in dock prepÆclick ok with default settings in “add hydrogen” windowÆclick ok for “specify net charges” windowÆa window as “save multiple files as mol2 format” will openÆgive the name of your choice and save with default setting “a single file[combined at molecule section]” 5. The file database is crated, right click and view the file in wordpad.
Compound Structure
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1. Amikacin
2. Aminosalicylic Acid
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3. Calcitriol
4. Capreomycin
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5. Cycloserine
6. Dihydrostreptomycin Sulfate
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7. Ethambutol
8. Ethionamide
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9. Iproniazid
10. Isoniazid
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11. kanamycin
12. pazufloxacin
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13. Prothionamide
14. Pyrazinamide
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15. Rifampin
16. Rifapentine
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17. Streptomycin
18. Thioacetazone
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19. thiobenzamide
20. Viomycin
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Result: The database created using UCSF Chimera. Ex no:10 Date:
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Chemical database creation using VEGAZZ
Aim: To create a chemical database using VEGAZZ.
URL: http://www.vegazz.net/
VEGAZZ: 1. VEGAZZ is the evolution of the well known VEGA OpenGL package. 2. It’s evolved to a complete molecular modeling suite. 3. It’s a free software. 4. It includes various calculation tools.
Steps involved:
1.Open VEGAZZ. 2.FileÆdatabseÆopenÆgive a database name you want to giveÆset “new database format” as sdf in right side of the windowÆclick create. 3.FileÆopenÆmolecule1Æopen molecule2Æ”new workspace”….continue for all the compounds…. 4.FileÆdatabaseÆexploreÆopen your database by clicking “open”Æget mode to “add” and click put for all the compounds shown in the tab belowÆclick done. 5.Open the database file.sdf in wordpad.
Result: The database created using VEGAZZ.
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