DERWENT MARKUSH RESOURCE DATABASE ON STN® Reference Manual February 2021 2 Authors: Andreas Barth Thomas Stengel Published by FIZ Karlsruhe – Leibniz Institute for Information Infrastructure Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Germany [email protected] www.fiz-karlsruhe.de © FIZ Karlsruhe 2020 These documents are intended for training purposes only. Copyright lies with FIZ Karlsruhe. Any distribution or use of these documents or part thereof beyond the aforementioned purposes is subject to FIZ Karlsruhe's express written approval. 3 Content 1. Introduction ........................................................................................................................ 7 1.1. DWPIM ON STNEXT AND NEW STN .................................................................................................. 9 1.1.1. Structure Search ............................................................................................................................ 9 1.1.1.1. Overview on attributes online and in transcripts .......................................................................... 9 1.1.1.2. Description of search types and modes ...................................................................................... 10 1.1.1.3. Iteration Incompletes .................................................................................................................. 11 1.1.1.4. Information after sample and structure search .......................................................................... 11 1.1.2. Display results ............................................................................................................................. 12 1.1.3. Substance Descriptors (SDM) and Markush Descriptors (MDE) .................................................. 14 1.1.4. Crossover from DWPIM to DWPI ................................................................................................ 14 1.1.5. Crossover of Compounds from DWPI to DWPIM ........................................................................ 15 1.1.6. Application of Roles in DWPI ....................................................................................................... 15 1.1.7. Application of Fragmentation Codes .......................................................................................... 15 1.1.8. Alert options ................................................................................................................................ 16 1.1.8.1. Automatic structure‐based alerts (SDI’s), including GUI support ............................................... 16 1.1.8.2. Use of scripts to upload structures and cross-over to DWPI ....................................................... 16 1.1.9. Subset Search .............................................................................................................................. 16 1.2. INCLUDED DATABASES – DERWENT CONTENT DOMAIN ........................................................................ 17 1.3. INDEXING LIMITATIONS ................................................................................................................... 20 1.4. WORKING EXAMPLE FOR INDEXING AND REPRESENTATION OF MARKUSH STRUCTURES IN DWPIM ............ 20 2. Derwent Markush Concept ............................................................................................... 27 2.1. CHEMICAL NODES .......................................................................................................................... 27 2.1.1. Atoms and the Derwent Element Groups .................................................................................... 27 2.1.2. Shortcuts ..................................................................................................................................... 28 2.1.3. Superatoms ................................................................................................................................. 29 2.1.4. Amino Acid Shortcuts .................................................................................................................. 34 2.2. VARIABLE GROUPS ......................................................................................................................... 35 2.3. CHEMICAL BONDS .......................................................................................................................... 35 2.3.1. Overview ..................................................................................................................................... 35 2.3.2. General STN Bond Conventions ................................................................................................... 37 2.3.3. Aromatic Bonds ........................................................................................................................... 37 2.3.4. Normalized Bonds in Ring Systems ............................................................................................. 38 2.3.5. Normalized Bonds in Tautomeric Systems .................................................................................. 39 2.3.5.1. Overview of Bond Normalization in Tautomers .......................................................................... 40 2.3.5.2. Special Case of Tautomerism and Aromaticity ........................................................................... 41 2.3.5.3. Special Case of Keto-Enol Tautomerism ...................................................................................... 42 2.3.5.4. Special Case of Vinyl Amine - Imine Tautomerization ................................................................. 43 2.3.5.5. Special Case of Quinoid Systems ................................................................................................. 43 2.4. NODE ATTRIBUTES ......................................................................................................................... 44 2.5. OTHER STRUCTURAL FEATURES ........................................................................................................ 45 2.5.1. Variable Points of Attachment .................................................................................................... 45 2.5.2. Repeating Groups ....................................................................................................................... 45 2.5.3. Additional Provisos...................................................................................................................... 46 4 3. STN Search Concept .......................................................................................................... 50 3.1. STN STRUCTURE BUILDING .............................................................................................................. 50 3.2. STN QUERY STRUCTURES ................................................................................................................ 53 3.3. SEARCH MODE AND SEARCH SCOPE .................................................................................................. 58 3.4. SPIN-OFF GENERIC NODES .............................................................................................................. 59 3.5. MATCH LEVELS .............................................................................................................................. 60 3.6. COMBINED HIERARCHY OF GENERIC NODES AND THE EFFECT OF MATCH LEVELS ...................................... 62 3.7. QUERY NODES ATTRIBUTES ............................................................................................................. 66 3.7.1. Mapping of STN Generic Group Attributes to Superatoms ......................................................... 66 3.7.2. Mapping of STN Generic Nodes to Superatoms .......................................................................... 67 3.7.3. Element Counts Limited and Unlimited ....................................................................................... 68 3.7.4. Impact of Superatom Attributes in the Node Hierarchy.............................................................. 71 3.8. OTHER SEARCH FIELDS .................................................................................................................... 72 3.8.1. Markush Compound Number ...................................................................................................... 72 3.8.2. DWPI Compound Number and DCR Compound Number Roles ................................................... 73 3.8.3. Role Searching Option of DCR and DWPIM Structure Search Results in DWPI ........................... 75 3.8.4. Substance Descriptors (SDM) ...................................................................................................... 75 3.8.5. Markush Descriptors (MDE) ........................................................................................................ 78 3.8.6. Patent Number Kind Code (PNK) ................................................................................................. 79 3.9. ATTRIBUTES ASSOCIATED WITH SUPERATOMS ..................................................................................... 79 3.10. ASSEMBLED DISPLAY .............................................................................................................. 82 3.11. FULL AND BRIEF DISPLAY ......................................................................................................... 83 3.12. MANUAL ASSEMBLING OF STRUCTURES ....................................................................................