Nomenclature of Phosphorus-Containing Compounds of Biochemical Importance (Recommendations 1976)*

Proc. Nati. Acad. Sci. USA Vol. 74, No. 6, pp. 2222-2230, June 1977 Biochemistry

Nomenclature of phosphorus-containing compounds of biochemical importance (Recommendations 1976)*

IUPAC-IUB COMMISSION ON BIOCHEMICAL NOMENCLATUREt

The IUPAC Commissions on the Nomenclature of Inorganic 2. Phosphate may be used for "(dihydrogen phosphate)," and of Organic Chemistry (CNIC and CNOC) have recently "(disodium phosphate)," etc., (a) if the nature of the counter- provided, in the "D-Rules" (1), recommendations for naming ions is not known or is of no importance in the context, or (b) a large number of organic compounds containing phosphorus. if a mixture of ionic forms (free acid and/or monoanion and/or Many such compounds are extremely important in biochem- dianion) is in question. Thus, in most biochemical or biological istry and hence in nearly all branches of biology and medicine. systems, where the pH is around 7, "glucose phosphate" may Most of the biochemically important ones are esters and/or be used in place of "glucose dihydrogen phosphate," the proper anhydrides of various phosphorus-containing acids with com- names for the protonated form. plex organic alcohols and organic acids. Strict application of the Comments. (i) Although glucose phosphate is an ester, the "D Rules" (1) to such compounds would result, in many cases, term "phosphate ester" should not be used: "phosphoric ester" in rather complicated names, and these would be inconvenient is the appropriate generic term. (ii) When "phosphoric" is for most biochemists and biologists to use. followed by a generic term (e.g., ester, amide, group), the word However, other systems of nomenclature, in use in the bio- "acid" need not intervene. Hence, "phosphoric ester" is com- chemical literature, are available (2-5). It is the purpose of this plete and sufficient, and the residue transferred to glucose to document to define and recommend certain of these for naming form 0-phosphonoglucose (see Section 1 above) is a "phosphoric organic phosphorus-containing compounds in biochemical, residue." (iii) To distinguish choline phosphate (ester) from biological, and medical publications. choline phosphate (salt), the former could be written "choline A general summary and explanation of the principles in- 0-phosphate." However, "phosphocholine" is unambiguous. volved in the nomenclature of biochemically important organic (For N-phosphono compounds, see Section 6.) phosphorus compounds is given below. Representative com- 3. Phosphoric anhydrides are of two types, (a) those in pounds and their recommended names, together with those which two or more phosphoric residues are linked by oxygen derived from more systematic nomenclature (4, 6, 7), including atoms to yield diphosphates, triphosphates, etc. (e.g., ADP, ATP, names formed according to the "D Rules" (1) where appro- etc.; Table 2) and (b) those in which phosphoric acid forms a priate, are listed in the tables. "mixed anhydride" with a different type of acid (generally a 1. Phosphoric esters, RO-PO(OH)2, are named as 0-sub- carboxylic acid, e.g., acetic acid) (Table 6). The latter are named stituted phosphoric acids or as substituted alcohols (Table 1). (ref. 1, Rule 5.64) as "R-ic phosphoric anhydrides" or as "R-yl Thus, choline 0-(dihydrogen phosphate) and 0-phosphono- phosphates" (e.g., acetic phosphoric anhydride or acetyl choline are both appropriate names. The latter may be con- phosphate). tracted to phosphocholine, but not changed to phosphoryl- Comments. (i). "Pyro" should not be used for the substituted choline; "phosphoryl" is defined (ref. 1, Rule 5.66) as OP< and phosphoric anhydrides (ref. 6, Rule 4.12) (Table 2), but may requires, if used, the naming of all three groups attached to the be retained in such terms as inorganic pyrophosphate (ref. 6, phosphorus atom. However, "phosphoryl" is retained in derived Rule 5.213), pyrophosphatase, pyrophosphate-glycerol trans- terms such as the names of enzymes (e.g., phosphorylase) or of ferase, and pyrophosphorolysis (2). (Compare Section 1 above processes (e.g., phosphorylation). re "phosphoryl".) Comment. The form 0-phosphono-R stems from two con- (ii) The prefixes di, tri, tetra, etc. should not be used to in- siderations, (i) the definition (ref. 1, Rule 5.51) of phosphonic dicate two or more independent phosphoric residues substituted acid as HPO(OH)2, and (ii) the principle in organic nomen- on different oxygen (or other) atoms in a single compound; the clature of substitution of another atom or group for a hydrogen appropriate multiplying prefixes for such compounds are bis, atom of a parent molecule, which, in this case, involves the tris, tetrakis, etc. (ref. 1, Rule 5.51; ref. 6, Rules 2.251 and 4.12). replacement of the H of an OH group by -P(O)(OH)2, the For example, "fructose 1,6-diphosphate" could indicate a di- phosphono group (ref. 1, Rule 5.52). phosphoric residue bridging positions 1 and 6 of fructose; the common biochemical substance is correctly named fructose * Document of the IUPAC-IUB Commission on Biochemical No- 1,6-bis(phosphate) (ref. 3, Rule 4.4). menclature (CBN),t approved by IUPAC and IUB in 1976 and published by permission of the International Union of Pure and 4. Phosphodiesters (Tables 3 and 4), which involve the Applied Chemistry (IUPAC) and the International Union of Bio-- bridging group -PO(OH)-, could be named in terms of phos- chemistry (IUB). Comments and suggestions for future revisions of phinic acid, H2PO(OH), for which the prefix form is phos- this document may be sent to any member of CBN.t Reprints may phinico (1). However, the use of this prefix, as in ref. 2, presents be obtained from the National Research Council Office of Bio- complications in placing the locants for unsymmetrical diesters. chemical Nomenclature (W. E. Cohn, Director), Biology Division, Hence, phosphinico is contracted to phospho, which is used as Oak Ridge National Laboratory, P.O. Box Y, Oak Ridge, TN 37830, U.S.A. an infix between the names of the two alcohols. Thus, glycer- t 0. Hoffmann-Ostenhof (Chairman), W. E. Cohn (Secretary), A. E. ophosphocholine is recommended (5) for the well-known Braunstein, H. B. F. Dixon, B. L. Horecker, W. B. Jakoby, P. Karlson, substance [previously (8), but incorrectly, called glycerophos- W. Klyne, C. Liebecq, and E. C. Webb. phorylcholine; compare Section 1 above]. This recommendation 2222 Downloaded by guest on October 2, 2021 Biochemistry: Commission on Biochemical Nomenclature Proc. Natl. Acad. Sci. USA 74 (1977) 2223 also illustrates the convention by which glycerol phPtbmUeis forbiochemnical use with "triphosphate" or "diphosphate" (see contracted to glycerophosphate (8), but this should not be done Table 8). in a context where "glycero" may be confused with the residue (v) The symbol for the nucleoside does not include the 5'- of glyceric acid, as in glycerolactone, or with the prefix glycero oxygen atom when the rest of the formula is written out in ex- used in carbohydrate nomenclature (ref. 4, Rule 9). (For the tenso. Thus, Ado(5')P[CH2]P Ado(5')-O-PO(OH)-CH2- placement of locants, see examples in Tables 1 and 4.) P03H2. Such extended representation may be useful for analogs Comments. (i) The use of "phosphoryl" in this situation re- such as Ado(5')-CH2-PO3H2, a methylene analog of AMP, and quires an indication in the name that there is one hydroxyl Ado(5')-O-PO(OH)-CH2-AsO3H2. group remaining on the phosphoric residue, and would thus 6. Phosphoric amides (Table 5) are named by changing further lengthen the name (see Section 1 above). "acid" in the original acid name to "amide" (ref. 1, Rule 5.62). (ii) The diacyl derivatives of glycerophosphocholine are However, when the nitrogenous group supplying the amide commonly expressed as derivatives of phosphatidic acid (Table moiety is known by a trivial name and that name is to be re- 4), i.e., diacylglycerophosphocholine phosphatidylcholine tained, the phosphoric amide may be named in the same (8). manner as the esters (see Section 1 above), but not in the form (iii) The trivial names for the acid radicals of nucleotides in which "phosphate" is used as a suffix (see Section 2 above); (Table 3) include the phosphoric residue, hence the latter is not e.g., phosphocreatine (for N-phosphonocreatine), but not specified in oligo- or polynucleotide names, e.g., adenylylcy- "creatine phosphate," because the term "phosphate" means tidine suffices for Ado-P-Cyd (locants omitted for clarity; cf. that all atoms attached to the phosphorus atom are oxygen ref. 9). atoms. (iv) The so-called cyclic phosphates (Table 3), of which Comment. The contraction "phosphoamide" for phosphoric adenosine 3',5'-phosphate (cyclic AMP or cAMP) is the best- amide is often seen, but becomes unwieldy when either the known example, are named in this form rather than in an in- amide or the phosphoric residue is substituted. Such compounds verted form, which would yield 3',5'-phosphoadenosine. The should be named as derivatives of phosphoramidic acid (or of word "cyclic," often added before "phosphate," is unnecessary a phosphoramidate), or of amidophosphoric acid (amido- if the locants are given. phosphate) [ref. 1, Rules 5.0(e), 5.53(a, b), and 5.61(a, b)]. (v) The infix "phospho" gives precedent for "diphospho," 7. Fluorophosphoric acids, when doubly esterified, become "triphospho," "tetraphospho," etc. for the doubly esterified fluorophosphates or phosphorofluoridates [ref. 1, Rules 5.53(a, oligophosphoric acids (Table 2), e.g., uridinediphosphoglucose, b), 5.61(a, b), and 5.0(e)]. Thus, the well-known compound adenosinediphosphoribose. (PriO)2PO-F or iPr2P-F (4) may be called diisopropyl fluoro- 5. Nucleoside Triphosphate Analogs, in which a methylene phosphate or diisopropyl phosphorofluoridate (see Table 6). group (-CH2-), an imido group (-NH-), or a sulfur atom replaces an oxygen atom bridging two phosphorus atoms, could 1. "Nomenclature of Organic Chemistry, Section D," IUPAC In- be named by an extension of the convention of inorganic no- formation Bulletin, Appendix 31, August 1973, pp. 60-86. menclature (ref. 6, Rule 4.15) that employs ,u to indicate a 2. Enzyme Nomenclature (1972), (Elsevier Scientific Publishing bridging group. Thus the compound symbolized as Ado- Company, Amsterdam and New York), [Supplement 1: Biochim. (5')P[CH2JPP could be named adenosine 5'-(1,2-,u-meth- Biophys. Acta 429,1-45 (1976)1. ylene)triphosphate, and Ado(5')PP[CH2]P might be named 3. "Abbreviations and Symbols for Chemical Names of Special adenosine However, for the Interest in Biological Chemistry" (1965 Tentative Rules); Bio- 5'-(2,3-,u-methylene)triphosphate. chem. J. 101, 1-7 (1966); Biochemistry 5,1445-1453 (1966); and "methylene" part of these names, [a,f-methylene] and [03,y- elsewhere. methylenel are unambiguous, are consistent with the use of 4. "Nomenclature of Carbohydrates" (1969), Biochemistry 10, Greek letters as locants in other situations (7), and are therefore 3983-4004 (1971); Eur. J. Biochem. 21, 455-477 (1971); and recommended (see Table 8). (The latter compound can be elsewhere. termed 5'-adenylyl methylenediphosphonate, but this name 5. "Nomenclature of Lipids" (1976), Hoppe-Seyler's Z. Physiol. does not contain the significant term "triphosphate".) Chem., in press; Lipids 12, 455-468 (1977). Comments. (i) The use of square brackets here is similar to 6. IUPAC Nomenclature of Inorganic Chemistry, (1970) (But- their use in amino-acid replacement (11), indicating a re- terworths, London). of the normal constituent. 7. IUPAC Nomenclature of Organic Chemistry, Sections A, B, C, placement (1971) (Butterworths, London). (ii) Although the bridging methylene group in the Ado- 8. "The Nomenclature of Lipids" (1967), J. Biol. Chem. 242, (5')PP[CH2]P example should receive priority for numbering, 4845-4849 (1967); and 245, 1511 (1970); and elsewhere. Revision i.e., should be 1,2-,-methylene to accord with inorganic no- (1976), in press (5). menclature (ref. 6, Rule 4.15), this would require an additional 9. "Abbreviations and Symbols for Nucleic Acids, Polynucleotides, term (as in Table 8, column 2); it is therefore not suitable in this and their Constituents" (1970), Arch. Biochem. Biophys. 145, context, in which it is desirable to give adenosine first consid- 425-436 (1971); Eur. J. Biochem. 15,203-208 (1970); and else- eration (i.e., it is always considered to be linked to the a phos- where. phorus atom). 10. "Symbols for Amino-Acid Derivatives and Peptides" (Recom- (iii) A terminal substitution (e.g., sulfur replacing oxygen on mendations 1971), Biochim. Biophys. Acta 263,205-212 (1972); be named adenosine J. Biol. Chem. 247, 977-983 (1972); and elsewhere. P3) might 5'-[3-thiojtriphosphate, but 11. "Rules for Naming Synthetic Modfications of Natural Peptides" adenosine 5'-y-thioJtriphosphate is recommended (see ii (Tentative Rules 1966, amended 1972), Biochemistry 6,362-364 above). (1975); and elsewhere. (iv) The rules of inorganic nomenclature (ref. 6, Table II) 12. "Nomenclature of (Y-Amino Acids" (Recommendations 1974), specify "imido" as the ligand name for -NH-; it is, in this case, Biochemistry 14, 449-462 (1975); Biochem. J. 149,1-16 (1975); an imide of phosphoric acid, hence "imido" is recommended and elsewhere. Downloaded by guest on October 2, 2021 2224 Biochemistry: Commission on Biochemical Nomenclature Proc. Natl. Acad. Sci. USA 74 (1977)

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Table 4. Representative phospholipids (involving diesterified phosphoric acid) Recommended nameab Other names AbbreviationsC Structure 1. sn-Glycero(3)phosphocholine Glycerol choline phosphate GroPCho 'CH.,OH 21 HO_-CH 3CH.O-P-OCH2CH2N(CH3),.1 + 2 1 2. (3-sn-Phosphatidyl)choline 1,2-Diacyl-sn-glycero( 3 )phos- PtdCho; 'CH2O2CR phocholine; lecithin d acyl2 GroPCho I RCO2mkH2 ~~~~+ 31 3CH.o-P-OCH2CH2N(CH3)3 3. (3-sn-Phosphatidyl )-L-serine 1,2-Diacyl-sn-glycero(3 )-L-phos- PtdSer; CH202CR phoserine; cephalind acyl2GroPSer RCO.,-CH NH2 CH20-P-OH2CHCO2H 4. (3-sn-Phosphatidyl)ethanol- 1 ,2-Diacyl-sn-glycero(3 )phos- PtdEtn; 'CH202CR amine phoethanolamine; cephalind acyl2GroPEtn 2 1 RCG02'CH 3CHO-P-OCH2CH2NH2 5. 2-Acyl-1-(1-alkenyl)-sn- Plasmenylcholine e; 'CH2OCH=-CHR glycero(3 )phosphocho- plasmalogen 21 line RCO,_-CH 3CH,O-P-OCH2CH2N(CH3)231 ~~~~~+ 6. 1-(3-sn-Phosphatidyl )-sn- 1, 2-Diacyl-sn-glycero(3 )- PtdGro ICH202CR 3CH20H 21 glycerol phospho(1 )-sn-glycerol RCO2.'-CH HC-9OH 3CH.,O-P-OCH2,1 7. 1-(3-sn-Phosphatidyl)- 1,2-Diacyl-sn-glycero(3 )- Ptdlns L-myo-inositol phospho( 1 )-L-myo- inositol; phosphoinositided 8. 1-(3-sn-Phosphatidyl )- 1,2-Diacyl-sn-glycero(3 )phos- PtdIns4P 'CH,2OCR L-myo-inositol 4-phospho(1)-L-myo-inositol 4- 21 phate phosphate; RCO2b_-CH 31 1 ,2-diacyl-sn-glycero(3)phos- CHlO-P-O OH OH pho( 1 )-4-phospho-L- myo-inositol; OH phosphoinositide 4-phos- HO phate d; diphosphoinositide d O-P 9. 1-(3-sn-Phosphatidyl)- 1,2-Diacyl-sn-glycero(3 )phos- PtdIns(3,4 )P2 1CH202CR L -myo-inositol pho(1)-L-myo-inositol 3,4- 21 3,4-bis(phosphate) bis(phosphate); RCO2m-CH 1,2-diacyl-sn-glycero(3 )- 3CH 0-P-O OH phospho(1 )-3,4-bis(phospho)- O-P L-myo-inositol; 54 1)hosphoinositide 3,4-bis- (phosphate)d; triphospho- 0-P d ' CHOH inositide 21 10. sn-Glycero(3)-2- sn-Glycerol 3-[ ( 2-aminoethyl )- GroPEtNH2 HO_-CH phosphonoethylamine f phosphonate ] 2 3CHO-P-HCH2CHNH2 11. (3-sn-Phosphatidyl )- 1 ,2-Diacyl-sn-glycero(3 )-2- PtdEtNH2 ' CH2O2CR f ethylamine phosphonoethylamine RCO2 _CH 2 1 3CH20-P-CH2CH2NH2

a Stereospecific numbering denoted by sn is defined in ref. 8. If fully defined in a paper, sn and various locants and descriptors may be omitted from the recommended names and abbreviations. The infix "phospho" replaces "phosphoryl" and "phosphinico," which have been used in the past (refs. 2 and 3) (see Sections 1 and 4 of the text). b Phosphatidyl = 1,2-diacyl-sn-glycero(3)phospho, which may replace it when desired. For O-alkenyl- and O-alkyl-substituted glycero compounds ("lyso" compounds), see entry 5 and ref. 5. c The symbols Ptd for phosphatidyl, Gro for glycerol, Cho for choline, Ser for serine, Etn for ethanolamine, Ins for inositol, and P for a phosphoric residue are defined in ref. 5. d Trivial names occasionally used in the past; not recommended. Included here only for reference. e Plasmenyl and plasmanyl are defined in ref. 5. f Phosphonic derivatives, containing a P-C bond (compare entry 4, also Table 7). Downloaded by guest on October 2, 2021 Biochemistry: Commission on Biochemical Nomenclature Proc.- Natl. Acad. Sci-. USA 74 (1977) 2229

Table 5. Phosphoric amides (phosphoramidic acids or amidophosphoric acids) Recommended namesa Other namesbc Structure

1. Phosphocreatine NL- -Phosphonocreatine; NH CH3 N-(N-Phosphonoamidino) sarcosine P-NHC-NCHICOH 2. Phosphoglycocyamine NW -Phosphonoglycocyamine; NH NL -phosphonoguanidinoacetic acid; NN N-(N-phosphonoamidino)glycine P-NHCNHCHC0,H 3. Phosphoguanidine N-Amidinophosphoramidate; NH N-amidinophosphoramidic acid P INHCNH, 4. pros-Phosphohistidined; 3(1)-PhosphonohistidineC VN ir-phosphohistidine NH CHXCHCO.,H 5. tele-Phosphohistidined; 1(3)-PhosphonohistidineC P T-phosphohistidine ~N HINH2 CHCHCO2H a See Section 6 of the text for a discussion of the reasons for not using the "phosphate" form of name for the phosphoric amides. P-Creatine and creatine-P are valid for abbreviation purposes, on the assumption that the hyphen indicates a covalent bond; names such as creatine phosphate do not indicate a covalent bond. b The symbol w is used to mean the NH2 terminal group. c The prefix "phosphonato" may be used to indicate an ionic form (ref. 1, Rule 5.52). d For definition of pros (r) and tele (T) locants, see refs. 10 and 12. Table 6. Representative phosphoric anhydrides and fluorophosphatesa Recommended names Other names Abbreviations Structure 1. Acetyl phosphate Monoacetyl phosphate; acetic Ac-P CHC0,-P phosphoric monoanhydride 2. p-Aspartyl phosphate Mono-,B-aspartyl phosphate; Asp(OP) NH2 B-aspartic phosphoric H

monoanhydride a P 3. Carbamoyl phosphateh Monocarbamoyl phosphate; Cbm-P HNCO,-P carbamic phosphoric monoanhydride 4. Adenosine 5'-phosphosulfate Adenosine 5'-P-phosphatosul- AP~d; HOSO-P-OCH, Ade fatec; 5'-adenylyl sulfate; AdoPS 5'-adenylic sulfuric monoanhydride HO OH 5. Adenosine 3'-phosphate 5'- Adenosine 3'-phosphate 5'-P- PAPSd; A phosphosulfate; phosphatosulfatec; 3'-phos- PAdoPS H P A 3'-phosphoadenosine 5'- pho-5'-adenylyl sulfate; phosphosulfate 3'-phospho-5'-adenylic P-O OH sulfuric monoanhydride 6. Seryl adenylate 1-0-(5'-Adenylyl)serine; AMP-Ser; NH2 adenosine(5' )phospho(1)- Ser-P-Ado A serine HOCHCHCO2-P-OCH2 0 Ade

*HO OH 7. 3-Phosphoglyceroyl phos- 3-0-Phosphonoglyceric phos- Gri(1,3)Pf P OCH2CH(OH)CO,-P phatee phoric monoanhydride; (glyceroyl phosphate) 3-phosphate 8. Diisopropyl fluorophosphate Diisopropyl phosphorofluori- iPr2P-Fg [(CH,),CHojP(O)F date

a See Sections 3 and 7 in text. b "Carbamyl," which is often used, is not in accord with the Organic Rules (ref. 10, Rule 431.2). c See Rules of Inorganic Nomenclature (ref. 6, Rule 4.211). d Commonly used in the literature; Ado form is preferred for A and P and S for the acid residues. e See entry 16 in Table 1. f See footnote b in Table 1. g Equivalent to DIPF, FDIP, DFP, and Dip-F (ref. 10). Downloaded by guest on October 2, 2021 2230 Biochemistry: Commission on Biochemical Nomenclature Proc. Natl. Acad. Sci. USA 74 (1977)

Table 7. Representative C-phosphonates Recommended name Other namesa Structure 1. (2-Aminoethyl)phosphonic acidb 2-Phosphonoethylamine; p H1H2 ciliatine 2. (2-Oxoethyl)phosphonic acid (Formylmethyl)phosphonic acid; P-CH2CHO phosphonoacetaldehyde

a The prefix "phosphonato" may be used to indicate an ionic form (ref. 1, Rule 5.52). b See also entries 10 and 11 in Table 4.

Table 8. Adenosine 5'-triphosphate analogsa Recommended name Other namesb Abbreviations Structure 1. Adenosine 5'-[a,,s-methylene]- Adenosine (5'-0)-1,2-M- AdoP[CH2]PP; 'P A H P OA triphosphate methylenetriphosphate; pp[CH21pA POP-CH2-P-OCH2 o Ade adenosine (5'-P')-1,2-,u- methylenetriphosphate HO OH 2. Adenosine 5--[3,'y-imido]- Adenosine (5'-03)-,2-,u- AdoPP[NH]P; 'r a 6' triphosphate imidotriphosphate; p[NH] ppA P NH-POP-OCH2 0 Ade adenosine (5'-P3)-1,2- ,u-imidotriphosphate; HO OH 5'-adenylyl imidodi- phosphate; 5'-adenylyl iminodi- phosphonatec 3. Adenosine 5'-[,y-thio]- Adenosine-(5'-0)-1- AdoPPP[S]; O$PO-POP-0CH, o Ade triphosphate thiotriphosphate; [S]pppA; I / \ dI adenosine (5'-P3)-1- ATP[S] thiotriphosphate HO OH

a See Section 5 in text. b Adaptation of principles of inorganic nomenclature for isopolyanions (ref. 6, Rule 4.15). c "Iminodiphosphonate" is derived from organic nomenclature principles (ref. 7, Rules B-15.1, C-815.1). Downloaded by guest on October 2, 2021