Miguel wrote: > I just checked in code which defines the nucleic-related things. > The definitions are equivalent to the following: > > define a [A],[+A] > define g [G],[+G] > define c [C],[+C] > define t [T],[+T] > > define i [I],[+I] > define u [U],[+U] > > define purine [A],[+A],[G],[+G],[I],[+I] > define pyrimidine [C],[+C],[T],[+T],[U],[+U] > > define nucleic [A],[+A],[G],[+G],[C],[+C],[T],[+T],[I],[+I],[U],[+U],\ > [1MA],[5MC],[OMC],[1MG],[2MG],[M2G],[7MG],[OMG],[YG],[H2U],[5MU],[PSU] > > Please let me know if there are problems with this.
I would suggest to include all purine and pyrimidine derivates into this set as a long term target and think we need a real chemist to review the following lists. I've looked in detail at Cysteine using http://www.imb-jena.de/ImgLibPDB/pages/hetDir/hetDir.php3?hetDirTab=hetDir&field=name&name=cytosine they all look like I expect pyrimidines should look (but I'm not a chemist) 1MC 1-METHYLCYTOSINE 1bky only the base without sugar 3MC 3-METHYLCYTOSINE 3MCT only the base without sugar C66 2-AMINOETHYLLYSINE-CARBONYLMETHYLENE-CYTOSINE 1nr8 no sugar CAR CYTOSINE ARABINOSIDE 1nh3 with arabinose (ribose isomer) CP1 2-(METHYLAMINO)-ETHYLGLYCINE-CARBONYLMETHYLENE- CYTOSINE 1QPY no sugar CPN 2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-CYTOSINE 1nr8 no sugar DFC 2'-DEOXY-L-RIBO-FURANOSYL CYTOSINE-5'-MONOPHOSPHATE 1r4d deoxy sugar IMC 2'-DEOXY-5-METHYLISOCYTOSINE 1be5 MCN PTERIN CYTOSINE DINUCLEOTIDE 1N62 PCD (MOLYBDOPTERIN-CYTOSINE DINUCLEOTIDE-S,S)-DIOXO-AQUA-MOLYBDENUM(V) 1FFV doing the same search for thymidine (but I don't look at detail into that) group name formula an PDB example 2DT 3'-DEOXYTHYMIDINE-5'-MONOPHOSPHATE C10 H15 N2 O7 P1 1qtm 5AT 5'-AMINO-5'-DEOXYTHYMIDINE 2(H15 C10 N3 O4) 1c95 5HT 5-HYDROXY-THYMIDINE C10 H16 N2 O6 1ehl 5IT 5-IODO-THYMIDINE-5'-PHOSPHATE C9 H12 N2 O8 I1 P1 1a6y 64T 5-HYDROXY-THYMIDINE-5'-MONOPHOSPHATE C10 H17 N2 O9 P1 1keg 6CT 6-ALPHA-METHYL CARBOCYCLIC THYMIDINE 2(C12 H18 N2 O6 P1) 1dau ABT 3'-AZIDO-3'-DEOXY-THYMIDINE-5'-ALPHA BORANO TRIPHOSPHATE 2(C10 H17 B1 N5 O12 P3) 1mn7 ADT N-ACETYL-DEOXYTHYMIDINE (SEE REMARK 7) 2(C12 H17 N3 O5) 8rsa ATD THYMIDINE-3'-PHOSPHATE 2(C10 H15 N2 O8 P1) 1bx5 ATM 3'-AZIDO-3'-DEOXYTHYMIDINE-5'-MONOPHOSPHATE C10 H14 N5 O7 P1 1e98 ATY 3'-O-ACETYLTHYMIDINE-5'-DIPHOSPHATE C12 H18 N2 O12 P2 1dzt AZD 3'-AZIDO-3'-DEOXYTHYMIDINE-5'-DIPHOSPHATE 3(C10 H15 N5 O10 P2) 1lwx AZT 3'-AZIDO-3'-DEOXYTHYMIDINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 8ico D4D 2',3'-DEHYDRO-2',3'-DEOXY-THYMIDINE 5'-DIPHOSPHATE C10 H13 N2 O10 P2 1f3f D4T 2',3'-DEHYDRO-2',3'-DEOXY-THYMIDINE 5'-TRIPHOSPHATE 3(C10 H14 N2 O13 P3) 1f3f DAU 2'DEOXY-THYMIDINE-5'-DIPHOSPHO-ALPHA-D-GLUCOSE 16(C16 H26 N2 O16 P2) 1g1l DRT 2'-DEOXY-L-RIBO-FURANOSYL THYMIDINE-5'-MONOPHOSPHATE C10 H15 N2 O8 P1 1fv8 FDM 3'-FLUORO-3'-DEOXYTHYMIDINE MONOPHOSPHATE C10 H14 N2 O7 F1 P1 1nmx MMT 5'-O-(DIMETHYLAMINO)-THYMIDINE H19 C12 N3 O5 1cx5 NYM 3'-DEOXY-3'-AMINOTHYMIDINE MONOPHOSPHATE C10 H16 N3 O7 P1 1nmz PST P-THIOTHYMIDINE C10 H14 N2 O6 P1 S1 1krp PTP DEOXYTHYMIDINE-3',5'-BISPHOSPHATE C10 H13 N2 O11 P2 1enc SMT 2'-[(METHYLTHIO)ETHYLOXY]-THYMIDINE-5'-MONOPHOSPHATE 2(C13 H21 N2 O9 P1 S1) 1mlx SPT 5'-THIO-THYMIDINE PHOSPHONIC ACID C10 H15 N2 O7 P1 S1 1k4s T THYMIDINE-5'-MONOPHOSPHATE C10 H15 N2 O8 P1 1mw8 T2S THYMIDINE-5'-DITHIOPHOSPHORATE C10 H15 N2 O6 P1 S2 1k8l T3P ALPHA-ANOMERIC THYMIDINE-3'-PHOSPHATE C10 H15 N2 O8 P1 1c2q TBD 2*-DEOXY-THYMIDINE-5*-ALPHA BORANO DIPHOSPHATE (ISOMER RP) 3(C10 H19 N2 O10 P2 B1 -1) 1f6t TCP 5'-METHYLTHYMIDINE C11 H16 N2 O5 1ac3 TDX THYMIDINE-5'-DIPHOSPHO-BETA-D-XYLOSE 2(C15 H24 N2 O15 P2) 1kep THM THYMIDINE C10 H14 N2 O5 1e2j THP THYMIDINE-3',5'-DIPHOSPHATE C10 H16 N2 O11 P2 1a2t THS THYMIDINE-5'-(DITHIO)PHOSPHATE 3(C10 H15 N2 O6 P1 S2) 1ak0 TMP THYMIDINE-5'-PHOSPHATE 2(C10 H15 N2 O8 P1) 1cy1 TPE 3'-O-ACETYLTHYMIDINE-5'-(DIPHOSPHATE PHENYL ESTER) C18 H23 N2 O12 P2 1dzt TRH 2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE 8(C16 H26 N2 O15 P2) 1g3l TSP 3'-THIO-THYMIDINE-5'-PHOSPHATE C10 H15 N2 O7 P1 S1 1ac3 TTP THYMIDINE-5'-TRIPHOSPHATE C10 H17 N2 O14 P3 1cr1 TYD THYMIDINE-5'- DIPHOSPHATE C10 H16 N2 O11 P2 1cr4 for uracil I got 612 6-CYCLOHEXYLTHIO-1-ETHOXYMETHYL-5-ISOPROPYLURACIL C16 H20 N2 O3 S1 1c1c AHU 1',5'-ANHYDRO-2',3'-DIDEOXY-2'-(5-IODOURACIL-1-YL)- D-ARABINO-HEXITOL 2(C10 H13 N2 O5 I1) 1ki6 GCA 6-(3',5'-DIMETHYLBENZYL)-1-ETHOXYMETHYL-5- ISOPROPYLURACIL C19 H26 N2 O3 1c1b HMU 5-HYDROXYMETHYL URACIL 2(C5 H6 N2 O3) 1oe6 IUR 5-IODOURACIL 4(C4 H3 N2 O2 I1) 1gte MKC 6-BENZYL-1-ETHOXYMETHYL-5-ISOPROPYL URACIL C17 H22 N2 O3 1rt1 PFA [4-(4-HYDROXY-3-ISOPROPYL-PHENOXY)-3,5-DIMETHYL- PHENYL]-6-AZAURACIL 2(C20 H21 N3 O4) 1n46 SUR 1-(BETA-D-RIBOFURANOSYL)-2-THIO-URACIL-5'- PHOSPHATE 4(C9 H13 N2 O8 P1 S1) 1hdw TNK 6-BENZYL-1-BENZYLOXYMETHYL-5-ISOPROPYL URACIL C22 H24 N2 O3 1jla UAA URACIL-6-ACETIC ACID 4(C6 H6 N2 O4) 1gt8 UAR URACIL ARABINOSE-5'-PHOSPHATE C9 H13 N2 O9 P1 1ho6 URA URACIL 4(C4 H4 N2 O2) 1bd4 URF 5-FLUOROURACIL 4(C4 H3 N2 O2 F1) 1h7x additional search for pyrimidine 141 PYRAZOLO[3,4-D]PYRIMIDINE-4,6-DIONE 4(C5 H2 N4 O2) 1jrp 7HP 7-HYDROXY-PYRAZOLO[4,3-D]PYRIMIDINE 2(C5 H4 N4 O1) 1i0i BBH 1-BENZYL-3-(4-METHOXY-BENZENESULFONYL)-6-OXO- HEXAHYDRO-PYRIMIDINE-4-CARBOXYLIC ACID HYDROXYAMIDE C19 H21 N3 O6 S1 1d8m BBT 2-HYDROXY-5-[4-(2-HYDROXY-ETHYL)-PIPERIDIN-1-YL]-5- PHENYL-1H-PYRIMIDINE-4,6-DIONE C17 H21 N3 O4 1jj9 CCV 6-[3-HYDROXY-2-(HYDROXYMETHYL)PROPYL]-5-METHYL- 2,4(1H,3H)-PYRIMIDINEDIONE 2(C9 H14 N2 O4) 1e2p COE FURO[2,3D]PYRIMIDINE ANTIFOLATE C20 H22 N6 O6 1daj COQ 2,4-DIAMINO-6-[N-(3',5'-DIMETHOXYBENZYL)-N- METHYLAMINO]PYRIDO[2,3-D]PYRIMIDINE C17 H20 N6 O2 1ly4 CP6 5-(4-CHLORO-PHENYL)-6-ETHYL-PYRIMIDINE-2,4-DIAMINE 2(C12 H13 N4 CL1) 1j3j DDP 2,4-DIAMINO-4,6-DIHYDROXYPYRIMIDINE C4 H6 N4 O2 1il5 DTM 2,4-DIAMINO-6-[N-(3',4',5'-TRIMETHOXYBENZYL)-N- METHYLAMINO]PYRIDO[2,3-D]PYRIMIDINE C18 H22 N6 O3 1mvs DUC DIHYDROPYRIMIDINE-2,4(1H,3H)-DIONE 2(C4 H6 N2 O2) 1uaq FQP 4-AMINO-2-TRIFLUOROMETHYL-5-HYDROXYMETHYLPYRIMIDINE PYROPHOSPHATE 2(C6 H8 N3 O7 F3 P2) 1g4p HMH 4-AMINO-5-HYDROXYMETHYL-2-METHYLPYRIMIDINE 2(C6 H9 N3 O1) 1jxi HQQ 5-METHYL-5-(4-PHENOXY-PHENYL)-PYRIMIDINE-2,4,6-TRIONE 3(C17 H14 N2 O4) 1g4k IDH (5S)-5-IODODIHYDRO-2,4(1H,3H)- PYRIMIDINEDIONE 2(C4 H5 N2 O2 I1) 1gth INI 5-NITRO-6-RIBITYL-AMINO-2,4(1H,3H)-PYRIMIDINEDIONE 30(C9 H14 N4 O8) 1rvv LIH 6-([5-QUINOLYLAMINO]METHYL)-2,4-DIAMINO-5- METHYLPYRIDO[2,3-D]PYRIMIDINE C18 H17 N7 1kms LII (Z)-6-(2-[2,5-DIMETHOXYPHENYL]ETHEN-1-YL)-2,4-DIAMINO- 5-METHYLPYRIDO[2,3-D]PYRIMIDINE C18 H19 N5 O2 1kmv LMZ 5-NITROSO-6-RIBITYL-AMINO-2,4(1H,3H)-PYRIMIDINEDIONE 20(C9 H14 N4 O7) 1c2y NW1 6-CYCLOHEXYLMETHYLOXY-5-NITROSO-PYRIMIDINE-2, 4-DIAMINE C11 H17 N5 O2 1e1x PQ0 2-AMINO-4-OXO-4,7-DIHYDRO-3H-PYRROLO[2,3-D]PYRIMIDINE- 5-CARBONITRILE C7 H5 N5 O1 1it8 PRD N6-(2,5-DIMETHOXY-BENZYL)-N6-METHYL-PYRIDO[2,3- D]PYRIMIDINE-2,4,6-TRIAMINE C17 H20 N6 O2 1boz RCA 6-{[4-(HYDROXYMETHYL)-5-METHYL-2,6-DIOXOHEXAHYDROPYRIMIDIN-5-YL] METHYL}-5-METHYLPYRIMIDINE-2,4(1H,3H)-DIONE C12 N4 O5 H16 0 1e2n TMC 1-[4-HYDROXY-5-(HYDROXYMETHYL)BICYCLO[3.1.0] HEX-2-YL]-5-METHYLPYRIMIDINE-2,4(1H,3H)- DIONE 2(C12 H16 N2 O4) 1e2k for adenosine 101 2'-DEOXY-ADENOSINE 3'-MONOPHOSPHATE C10 H14 N5 O6 P1 1cs4 103 2',5'-DIDEOXY-ADENOSINE 3'-MONOPHOSPHATE C10 H14 N5 O5 P1 1cul 12A 2-METHYLTHIO-N6-(AMINOCARBONYL-L-THREONYL)-ADENOSINE- 5'-MONOPHOSPHATE C16 H26 N5 O7 P1 S1 1fir 139 ADENOSINE-5'-[TRIHYDROGEN DIPHOSPHATE] P'-3'-ESTER WITH 2'-DEOXYURIDINE C19 H25 N7 O14 P2 1jn4 1DA 1-DEAZA-ADENOSINE C11 H14 N4 O4 1add 1MA 6-HYDRO-1-METHYLADENOSINE-5'-MONOPHOSPHATE 2(C11 H18 N5 O7 P1) 1c2w 2AD 2-AMINO-ADENOSINE C10 H14 N6 O3 1obc 2DA 2',3'-DIDEOXYADENOSINE-5'-MONOPHOSPHATE C10 H14 N5 O5 P1 1qsy 2MA 2-METHYLADENOSINE-5'-MONOPHOSPHATE 2(C11 H16 N5 O7 P1) 1efw 3AD 3'-DEOXYADENOSINE 2(C10 H13 N5 O3) 1fa0 3AN 3'-DEOXY 3'-AMINO ADENOSINE-5'-DIPHOSPHATE 3(C10 H16 N6 O9 P2) 1hiy 3AT 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O12 P3 1f5a 5AD 5'-DEOXYADENOSINE 2(C10 H13 N5 O3) 4req 5CA 5'-O-(N-(L-CYSTEINYL)-SULFAMOYL)ADENOSINE C13 H19 N7 O7 S2 1nj1 8BR 8-BROMO-ADENOSINE-5'-MONOPHOSPHATE C10 H13 N5 O7 BR1 P1 5rhn A ADENOSINE-5'-MONOPHOSPHATE 8(C10 H14 N5 O7 P1) 1cvj A23 ADENOSINE-5'-PHOSPHATE-2',3'-CYCLIC PHOSPHATE C10 H13 N5 O9 P2 1d4r A2P ADENOSINE-2',5'-DIPHOSPHATE C10 H15 N5 O10 P2 1fnc A3P ADENOSINE-3'-5'-DIPHOSPHATE 2(C10 H15 N5 O10 P2) 1aqu A4P 6-(ADENOSINE TETRAPHOSPHATE-METHYL)-7,8-DIHYDROPTERIN C17 H24 N10 O17 P4 1ex8 A5A '5'-O-(N-(L-ALANYL)-SULFAMOYL)ADENOSINE C13 H19 N7 O7 S1 1nj6 AAM ALPHA-ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P1 1jha ABM METHYL PHOSPHONIC ACID ADENOSINE ESTER 2(C11 H16 N5 O6 P1) 1dku ABP 8-BROMOADENOSINE-5'-DIPHOSPHATE C10 H14 N5 O10 BR1 P2 1mxc ABR (R)-(N-PHENYL-2-HYDROXY-ETHYL)-2'-DEOXY-ADENOSINE-5'- MONOPHOSPHATE H22 C18 N5 O7 P1 1k5e ABS (S)-(N-PHENYL-2-HYDROXY-ETHYL)-2'-DEOXY-ADENOSINE-5'- MONOPHOSPHATE H22 C18 N5 O7 P1 1k5f ACO COBALAMIN-ADENOSINE COMPLEX C72 H100 N18 O17 CO1 P1 3req AD2 2'-DEOXY-ADENOSINE-3'-5'-DIPHOSPHATE C10 H15 N5 O9 P2 1l2b AD3 3-DEAZA-ADENOSINE 2(C11 H14 N4 O4) 1hp0 ADI 2',3'-DIDEOXYADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O8 P2 1jx4 ADN ADENOSINE 2(C10 H13 N5 O4) 1bx4 ADP ADENOSINE-5'-DIPHOSPHATE 4(C10 H15 N5 O10 P2) 13pk ADQ ADENOSINE-5'-DIPHOSPHATE-GLUCOSE 10(C16 H25 N5 O15 P2) 1eq2 ADS ADENOSINE-5'-(DITHIO)PHOSPHATE C10 H14 N5 O5 P1 S2 1ak0 ADW ADENOSINE-5'-DITUNGSTATE C10 H15 N5 O10 W2 1kpe ADX ADENOSINE-5'-PHOSPHOSULFATE 2(C10 H14 N5 O10 P1 S1) 1g8g ADY 3'-OXO-ADENOSINE 4(C10 H11 N5 O4) 1ky5 AMO ASPARTYL-ADENOSINE-5'-MONOPHOSPHATE C14 H19 N6 O10 P1 1c0a AMP ADENOSINE MONOPHOSPHATE 2(C10 H14 N5 O7 P1) 12as AMW ADENOSINE MONOTUNGSTATE C10 H14 N5 O7 W1 6fit AP2 ADENOSINE ALPHA,BETA-METHYLENE DIPHOSPHATE C11 H17 N5 O9 P2 1av5 AP5 PA,PE-BIS(ADENOSINE-5'-)PENTAPHOSPHATE 2(C20 H34 N10 O22 P5) 1ake APM 2'-DEOXYADENOSINE-5'- MONOPHOSPHATE 5(C10 H14 N5 O6 P1) 1lgn APR ADENOSINE-5-DIPHOSPHORIBOSE 2(C15 H23 N5 O14 P2) 1g9q APX 2'-MONOPHOSPHOADENOSINE-5'-DIPHOSPHORIBOSE 4(C15 H24 N5 O17 P3) 1qmg AS ADENOSINE-5'-THIO-MONOPHOSPHATE C10 H14 N5 O5 P1 S1 8psh ATA GAMMA-ARSONO-BETA, GAMMA-METHYLENEADENOSINE-5'- DIPHOSPHATE 2(C11 H19 N5 O12 AS1 P2) 1glj ATF ADENOSINE-5'-(BETA,GAMMA-DIFLUROROMETHYLENE) TRIPHOSPHATE 2(C11 H16 N5 O12 F2 P3) 1bwf ATG ADENOSINE 5'-O-(-3-THIOTRIPHOSPHATE) C10 H16 N5 O12 P3 S1 1bif ATP ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 1a0i ATR 2'-MONOPHOSPHOADENOSINE-5'-DIPHOSPHATE 2(C10 H16 N5 O13 P3) 1afl AV2 ADENOSINE-5'-DIPHOSPHATE-2',3'-VANADATE 2(C10 H13 N5 O12 P2 V1) 1m7g AVC ADENOSINE-5'-MONOPHOSPHATE-2',3'-VANADATE 2(C10 H12 N5 O9 P1 V1) 1m5o BIS (1,1,5,5-TETRAFLUORO-5-PHOSPHATE-PENTANE) ADENOSINE DIPHOSPHATE C15 H22 N5 O12 F4 P3 16pk CDY 2-CHLORODIDEOXYADENOSINE C10 H12 N5 O2 CL1 1qye CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE 2(C10 H12 N5 O6 P1) 1cx4 DAD 2',3'-DIDEOXYADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O11 P3 1cjt DAT 2'-DEOXYADENOSINE-5'-DIPHOSPHATE 2(C10 H15 N5 O9 P2) 1g4a DOT 3'ANTHRANILOYL-2'-DEOXY-ADENOSINE-5'-TRIPHOSPHATE 2(C17 H21 N6 O13 P3) 1lvc DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE C10 H12 N5 O12 P3 ---- 1bpe E 2'-DEOXY-N6-((-)-(7S,8R,9S,10R)[10-97,8,9,10-TETRA HYDROBENZO[A]PYRENYL]) ADENOSINE MONOPHOSPHATE C30 H28 N5 O9 P1 1agu FA5 ADENOSINE-5'-[PHENYLALANINYL-PHOSPHATE] C19 H23 N6 O8 P1 1jjc FYA PHENYLALANINYL-ADENOSINE-5'-PHOSPHATE C19 H25 N6 O7 P1 1b7y GAP GLYCYL-ADENOSINE-5'-PHOSPHATE 2(C12 H17 N6 O8 P1) 1ggm GTA P1-7-METHYLGUANOSINE-P3-ADENOSINE-5',5'-TRIPHOSPHATE C21 H30 N10 O17 P3 1+ 1ipb HAM HISTIDYL-ADENOSINE MONOPHOSPHATE 4(C16 H21 N8 O8 P1) 1ady HYC O5'-[9-(3,17B-DIHYDROXY-1,3,5(10)-ESTRATRIEN-16B-YL)- NONANOYL]ADENOSINE C37 H51 N5 O7 1i5r IB2 P1-P2-METHYLENE-P3-THIO-DIADENOSINE TRIPHOSPHATE C21 H29 N10 O14 P3 S1 1fhi IOT ARGININE-N-METHYLCARBONYL PHOSPHORIC ACID 5'- ADENOSINE ESTER 2(C18 H28 N9 O10 P1) 1mbz LAD ADENOSINE-5'-[LYSYL-PHOSPHATE] C16 H26 N7 O8 P1 1e1t MA6 6N-DIMETHYLADENOSINE-5'-MONOPHOSHATE 2(C12 H17 N5 O6 P1) 1wts MAD 6-HYDRO-1-METHYLADENOSINE-5'-MONOPHOSPHATE C11 H16 N5 O7 P1 1h3e MAO 5'-DEOXY-5'-[N-METHYL-N-(2-AMINOOXYETHYL) AMINO]ADENOSINE C13 H21 N7 O4 1i72 MHZ 5'-DEOXY-5'-[(3-HYDRAZINOPROPYL)METHYLAMINO]ADENOSINE C14 H24 N8 O3 1i79 MIA 2-METHYLTHIO-N6-ISOPENTENYL-ADENOSINE-5'-MONOPHOSPHATE C16 H26 N5 O7 P1 S1 1b23 MNT 2'(3')-O-N-METHYLANTHRANILOYL-ADENOSINE-5'-DIPHOSPHATE C18 H21 N6 O10 P2 1lvk MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE C11 H15 N5 O3 S1 1cg6 NBS N6-BENZYL ADENOSINE-5'-DIPHOSPHATE C17 H21 N5 O10 P2 1ksw NDE ADENOSINE 5'-(TRIHYDROGEN DIPHOSPHATE) P'-5'-ESTER WITH 3-(AMINOCARBONYL)-4-(1-HYDROXYL-2-OXO-3- PHOSPHONOOXY-PROPYL)-1-BETA-D-RIBOFURANOSYLPYRIDINIUM INNER SALT 2(C24 H32 N7 O20 P3) 1n1e NEA 5'-DEOXY-5'-[2-(AMINO)ETHYLTHIO]ADENOSINE 2(C12 H18 N6 O3 S1) 1g38 NEC N-ETHYL-5'-CARBOXAMIDO ADENOSINE C12 H16 N6 O4 1mmh NMD N-NAPHTHALEN-1-YLMETHYL-2'-[3,5-DIMETHOXYBENZAMIDO]- 2'-DEOXY-ADENOSINE 6(C30 H30 N6 O6) 1i32 OAD 2'-O-ACETYL ADENOSINE-5-DIPHOSPHORIBOSE 2(C17 H25 N5 O15 P2) 1m2n P5A '5'-O-(N-(L-PROLYL)-SULFAMOYL)ADENOSINE C15 H21 N7 O7 S1 1nj5 PAP 3'-PHOSPHATE-ADENOSINE-5'-DIPHOSPHATE 2(C10 H16 N5 O13 P3) 1afk PPS 3' PHOSPHATE-ADENOSINE -5' PHOSPHATE SULFATE 3(C10 H15 N5 O13 P2 S1) 1bux PRX ADENOSINE-5'-MONOPHOSPHATE-PROPYL ESTER 2(C13 H20 N5 O7 P1) 1pg3 PSD 5'-O-[N-(PROLYL)-SULFAMOYL]ADENOSINE 2(C15 H21 N7 O7 P1) 1h4s QSI 5'-O-[N-(L-GLUTAMINYL)-SULFAMOYL]ADENOSINE C15 H22 N8 O8 S1 1euq R 2'-DEOXY-N6-(R)STYRENE OXIDE ADENOSINE MONOPHOSPHATE C18 H22 N5 O7 P1 1agk RIA 2'-O-[(5'-PHOSPHO)RIBOSYL]ADENOSINE-5'- MONOPHOSPHATE C15 H22 N5 O14 P2 1yfg RMP 2'-DEOXY-ADENOSINE-5'-RP-MONOMETHYLPHOSPHONATE 3(C11 H16 N5 O5 P1) 1k1h SAP ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE 2(C10 H16 N5 O12 P3 S1) 1aux SMP 2'-DEOXY-ADENOSINE-5'-SP-MONOMETHYLPHOSPHONATE C11 H16 N5 O5 P1 1k1h SRA ADENOSINE -5'-THIO-MONOPHOSPHATE 5(C10 H14 N5 O6 P1 S1) 1d0t SSA 5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE 2(C13 H19 N7 O8 S1) 1fyf STP 2'-DEOXYADENOSINE 5'-O-(1-THIOTRIPHOSPHATE) C10 H16 N5 O11 P3 S1 9ica TND N-1,2,3,4-TETRAHYDRONAPHTH-1-YL-2'-[3,5- DIMETHOXYBENZAMIDO]-2'-DEOXY-ADENOSINE 6(C29 H32 N6 O6) 1i33 TSB 5'-O-(N-(L-THREONYL)-SULFAMOYL)ADENOSINE 4(C14 H21 N7 O8 S1) 1evl UP5 P1-(ADENOSINE-5'-P5-(URIDINE-5')PENTAPHOSPHATE C19 H28 N7 O24 P5 1uke UPA URIDYLYL-2'-5'-PHOSPHO-ADENOSINE 2(C19 H24 N7 O12 P1) 11ba Y 2'-DEOXY-N6-(S)STYRENE OXIDE ADENOSINE MONOPHOSPHATE C18 H22 N5 O7 P1 1ago for guanosine 1MG 1N-METHYLGUANOSINE-5'-MONOPHOSPHATE C11 H16 N5 O8 P1 1f7u 2GP GUANOSINE-2'-MONOPHOSPHATE 2(C10 H14 N5 O8 P1) 1bir 2MG 2N-METHYLGUANOSINE-5'-MONOPHOSPHATE C11 H16 N5 O8 P1 1ehz 35G GUANOSINE-3',5'-MONOPHOSPHATE 6(C10 H12 N5 O7 P1) 1bhn 3GP GUANOSINE-3'-MONOPHOSPHATE C10 H14 N5 O8 P1 2gsp 5CG 5'-CHLORO-5'-DEOXY-GUANOSINE 2(C10 H12 N5 O4 CL1) 1m5p 5GP GUANOSINE-5'-MONOPHOSPHATE 2(C10 H14 N5 O8 P1) 1a97 7MG 7N-METHYL-8-HYDROGUANOSINE-5'-MONOPHOSPHATE 3(C11 H18 N5 O8 P1) 1c2w 8MG 8-METHYL-2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE 2(C11 H16 N5 O7 P1) 1r4d 8OG 8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE C10 H14 N5 O8 P1 1fyi BGM 8-BROMO-2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE 8(C10 H13 N5 O7 P1 BR1) 1n7a CAG P3-1-(2-NITROPHENYL)ETHYL-GUANOSINE C18 H25 N6 O16 P3 1plj CPG CYTIDYLYL-2',5'-PHOSPHORYL GUANOSINE C10 H12 N5 O8 P1 1rnc DBG GUANOSINE-5'-(PHOSPHORAMIDATE-N- [[DIHYDROXYPHOSPHANYL]-IMINE-N-METHANE]) C11 H20 N7 O12 P3 1clu DCG DEOXYCYTIDYLYL-3',5'-GUANOSINE C10 H12 N5 O7 P1 - 1rnd DDG 2',3'-DIDEOXY-GUANOSINE-5'-MONOPHOSPHATE C10 H14 N5 O6 P1 1qss DFG 2'-DEOXY-L-RIBO-FURANOSYL GUANOSINE-5'-MONOPHOSPHATE 2(C10 H14 N5 O7 P1) 1fv7 DG3 2'-3'DIDEOXYGUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O12 P3 1jxl DGP 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE 2(C10 H14 N5 O7 P1) 1dek DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 8icv FAG 2'-DEOXY-N7-(8,9-DIHYDRO-8-(2,6-DIAMINO-4-OXO-3,4- DIHYDROPYRIMIDYL-5-FORMAMIDO)-9-(HYDROXY-AFLATOXINB1) GUANOSINE C27 H27 N5 O14 P1 1hm1 G GUANOSINE-5'-MONOPHOSPHATE C10 H14 N5 O8 P1 1g8m G25 GUANOSINE-5'-MONOPHOSPHATE C10 H14 N5 O8 P1 1me0 G2S GUANOSINE-5'-DITHIOPHOSPHORATE 2(C10 H14 N5 O6 P1 S2) 1k8l G3D GUANOSINE-3'-MONOPHOSPHATE-5'-DIPHOSPHATE C10 H16 N5 O14 P3 1mr3 G4P GUANOSINE-5',3'-TETRAPHOSPHATE C10 H17 N5 O17 P4 1lnz G7M N7-METHYL-GUANOSINE-5'-MONOPHOSPHATE C11 H17 N5 O8 P1 1+ 1c0a GDP GUANOSINE-5'-DIPHOSPHATE 3(C10 H15 N5 O11 P2) 1a2k GDR GUANOSINE-5'-DIPHOSPHATE-RHAMNOSE 3(C16 H25 N5 O15 P2) 1n7g GDX GUANOSINE 5'-(TRIHYDROGEN DIPHOSPHATE), P'-D- MANNOPYRANOSYL ESTER 4(C16 H23 N5 O17 P2) 1mfz GH3 3'-DEOXY-GUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 1n1h GMP GUANOSINE C10 H13 N5 O5 1ih7 GMS 2'-DEOXYGUANOSINE-5'-MONOSELENOPHOSPHATE 2(C10 H14 N5 O6 P1 SE1) 1n6s GN7 N7-GUANOSINE-5'-MONOPHOSPHATE C10 H14 N5 O7 P1 1gn7 GNG 2'-DEOXY-GUANOSINE C10 H13 N5 O4 1nh3 GP3 DIGUANOSINE-5'-TRIPHOSPHATE C20 H27 N10 O18 P3 1cko GPG GUANYLYL-2(PRIME),5(PRIME)-GUANOSINE C20 H24 N10 O12 P1 2rnt GPL LYSINE GUANOSINE-5'-MONOPHOSPHATE C16 H26 N7 O9 P1 1ckn GPX GUANOSINE 5'-DIPHOSPHATE 2':3'-CYCLIC MONOPHOSPHATE C10 H14 N5 O13 P3 1ch8 GS GUANOSINE-5'-THIO-MONOPHOSPHATE 3(C10 H14 N5 O6 P1 S1) 8psh GSP GUANOSINE DIPHOSPHATE MONOTHIOPHOSPHATE C10 H16 N5 O13 P3 S1 1a2b GSR 2'-DEOXY-N2-(R)STYRENE OXIDE GUANOSINE MONOPHOSPHATE C18 H22 N5 O8 P1 1af1 GSS 2'-DEOXY-N2-(S)STYRENE OXIDE GUANOSINE MONOPHOSPHATE C18 H22 N5 O8 P1 1ap1 GTA P1-7-METHYLGUANOSINE-P3-ADENOSINE-5',5'-TRIPHOSPHATE C21 H30 N10 O17 P3 1+ 1ipb GTG 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-GUANOSINE C21 H30 N10 O18 P3 +1 1mwh GTP GUANOSINE-5'-TRIPHOSPHATE 15(C10 H16 N5 O14 P3) 1a8r IG ISOGUANOSINE-5'-MONOPHOSPHATE 2(C10 H14 N5 O8 P1) 1g3a LGP LINEAR DECARBON-C2* GUANOSINE-5'-MONOPHOSPHATE C9 H14 N5 O7 P1 1ac9 M2G N2-DIMETHYLGUANOSINE-5'-MONOPHOSPHATE C12 H18 N5 O8 P1 1ehz M7G 7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE C11 H19 N5 O11 P2 1ap8 MDG 7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE C11 H19 N5 O11 P2 1jtf MG7 7-METHYLGUANOSINE C11 H16 N5 O5 1eqa MGD MOLYBDOPTERIN GUANOSINE DINUCLEOTIDE 2(C20 H24 N10 O13 P2 S2) 1aa6 MGP 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE C11 H19 N5 O14 P3 1+ 1ipc MGT 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE C11 H20 N5 O14 P3 1av6 MRG N2-(3-MERCAPTOPROPYL)-2'-DEOXYGUANOSINE-5'- MONOPHOSPHATE C13 H20 N5 O7 P1 S1 1n6q OMG O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE C11 H16 N5 O8 P1 1ehz P 2'-DEOXY-N1,N2-PROPANO GUANOSINE MONOPHOSPHATE C13 H18 N5 O7 P1 1ag3 PCG CYCLIC GUANOSINE MONOPHOSPHATE 3(C10 H12 N5 O7 P1) 1be4 PGD GUANOSINE-5'-DIPHOSPHATE PTERIN MOIETY OF MOLYBDOPTERIN GUANOSINE DINUCLEOTIDE 2(C20 H24 N10 O13 P2 S2) 1dmr PGN 2'-DEOXYGUANOSINE-3',5'-DIPHOSPHATE C10 H15 N5 O10 P2 1j9n PGP GUANOSINE-3',5'-DIPHOSPHATE C10 H15 N5 O11 P2 1duh PGS 2-DEAZO-6-THIOPHOSPHATE GUANOSINE-5'-MONOPHOSPHATE C10 H15 N4 O10 P2 S1 1ksz QUO 2-AMINO-7-DEAZA-(2'',3''-DIHYDROXY-CYCLOPENTYLAMINO)- GUANOSINE-5'-MONOPHOSPHATE C17 H26 N5 O10 P1 1c0a S6G 6-THIO-2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE C10 H14 N5 O6 P1 S1 1kb1 SGP GUANOSINE-2',3'-CYCLOPHOSPHOROTHIOATE C10 H12 N5 O6 P1 S1 1gsp SPG 2-DEAMINO-6-DEOXY-6THIOPHOSPHITE-5'-PHOSPHATE GUANOSINE C10 H15 N4 O10 P2 S1 1nht TGP 5'-THIO-2'-DEOXY-GUANOSINE PHOSPHONIC ACID C10 H14 N5 O6 P1 S1 1k4t U2G URIDYLYL-2'-5'-PHOSPHO-GUANOSINE 4(C19 H24 N7 O13 P1) 11bg X 2'-DEOXY-N7-(8,9-DIHYDRO-9-HYDROXY-AFLATOXIN) GUANOSINE MONOPHOSPHATE C27 H27 N5 O14 P1 1ag5 for inosine 9DI 9-DEAZAINOSINE C11 H13 N3 O5 1a9p IDP INOSINE-5'-DIPHOSPHATE C10 H14 N4 O11 P2 1mrd IMO 6-PHOSPHORYL INOSINE MONOPHOSPHATE C10 H9 N4 O11 P2 2- 1cg0 IMP INOSINE MONOPHOSPHATE 4(C10 H13 N4 O8 P1) 1abb NOS INOSINE C10 H12 N4 O5 1a9s OIP 2'-DEOXYINOSINE-5'-DIPHOSPHATE C10 H13 N4 O7 P1 1mrf aditional search for purine 1AP 2,6-DIAMINOPURINE NUCLEOTIDE C10 H15 N6 O6 P1 1zay 207 1-AMINO-6-CYCLOHEX-3-ENYLMETHYLOXYPURINE C13 H18 N4 O1 1h0w 2A6 2-ANILINO-6-CYCLOHEXYLMETHOXYPURINE 2(C18 H21 N5 O1) 1h1q 2SA 2-[9-(3,4-DIHYDROXY-5-PHOSPHONOOXYMETHYL-TETRAHYDRO- FURAN-2-YL)-9H-PURIN-6-YLAMINO]-SUCCINIC ACID C14 N5 O11 P1 H18 1mez 39A 6-AMINO-3,9-DIMETHYL-9H-PURIN-3-IUM 2(C7 H10 N5 1+) 1pu7 3MA 6-AMINO-3-METHYLPURINE C6 H8 N5 3mag 4SP O6-CYCLOHEXYLMETHOXY-2-(4'-SULPHAMOYLANILINO) PURINE 2(C18 H22 N6 O3 S1) 1h1s 6CP 6-CYCLOHEXYLMETHOXY-2-(3'-CHLOROANILINO) PURINE 2(C18 H23 N5 O1 CL1) 1h1r 6MP 6-METHYLPURINE C6 H6 N4 2pua 7RA 7-ALPHA-D-RIBOFURANOSYL-2-AMINOPURINE-5'-PHOSPHATE C10 H14 N5 O7 P1 1l5m 7RP 7-ALPHA-D-RIBOFURANOSYL-PURINE-5'-PHOSPHATE C10 H13 N4 O7 P1 1l5l 9PP 2,6-DIAMINO-(S)-9-[2-(PHOSPHONOMETHOXY)PROPYL]PURINE 6(C9 N6 O4 P1 H13 2-) 1lv8 AAD (2-AMINOOXY-ETHYL)-[5-(6-AMINO-PURIN-9-YL)-3,4- DIHYDROXY-TETRAHYDRO-FURAN-2-YLMETHYL]-METHYL- SULFONIUM C13 H21 N6 O4 S1 1+ 1m4n ADZ 9-METHYL-9H-PURIN-6-AMINE C6 H7 N5 1o9u AET N-[N-(9-B-D-RIBOFURANOSYLPURIN-6-YL) METHYLCARBAMOYL]THREONINE-5'-MONOPHOSPHATE C16 H23 N6 O11 P1 1qf6 BCP 2-BROMO-6-CHLORO-PURINE C5 H2 N4 CL1 BR1 1m66 BOA 2-BROMO-6-HYDROXY-PURINE C5 H3 N4 O1 BR1 1m67 CFP 6-CHLORO-2-FLUOROPURINE C5 H2 N4 CL1 F1 1jdj CL4 N-{3-[5-(6-AMINO-PURIN-9-YL)-3,4-DIHYDROXY-TETRAHYDRO- FURAN-2-YL]-ALLYL}-2,3-DIHYDROXY-5-NITRO-BENZAMIDE C19 H19 N7 O8 1jr4 CPR 6-CHLOROPURINE RIBOSIDE, 5'-MONOPHOSPHATE 2(C10 H13 N4 O7 P1 CL1) 1b3o EA1 3H-IMIDAZO[2,1-I]PURINE 2(C7 H5 N5) 1pu8 FTB N-{4-[1-(2-FLUOROBENZYL)-3-BUTYL-2,6-DIOXO-2,3,6,7- TETRAHYDRO-1H-PURIN-8-YLMETHYL]-PHENYL}-ACETAMIDE C25 H26 N5 O3 F1 1nhx GMC (2R,3R,4S,5S)-4-AMINO-2-[6-(DIMETHYLAMINO)- 9H-PURIN-9-YL]-5-(HYDROXYMETHYL)TETRAHYDRO-3- FURANOL C12 H18 N6 O3 1gpj GU7 2-AMINO-7-[2-(2-HYDROXY-1-HYDROXYMETHYL-ETHYLAMINO)- ETHYL]-1,7-DIHYDRO-PURIN-6-ONE C10 H16 N6 O3 1fxu HPR 6-HYDROXY-7,8-DIHYDRO PURINE NUCLEOSIDE C10 H14 N4 O5 1uio I17 2-[TRANS-(4-AMINOCYCLOHEXYL)AMINO]-6-(BENZYL-AMINO)-9- CYCLOPENTYLPURINE C23 H31 N7 1g5s LMS [(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4- DIHYDROXYTETRAHYDRO-2-FURANYL]METHYL SULFAMATE C10 H14 N6 O6 S1 1h3n M1A 6-AMINO-1-METHYLPURINE C6 H8 N5 1b42 M1G 3-(2-DEOXY-BETA-D-RIBOFURANOSYL)-PYRIDO[5,6-A]-PURINE- 10-ONE-5'-MONOPHOSPHATE C13 H14 N5 O7 P1 1k29 MBP 1-[(2-AMINO-6,9-DIHYDRO-1H-PURIN-6-YL)OXY]-3- METHYL-2-BUTANOL C10 H13 N5 O2 1gz8 NOC 3-(6-AMINO-PURIN-9-YL)-5-HYDROXYMETHYL-CYCLOPENTANE-1, 2-DIOL C11 H15 N5 O3 1li4 NRT 6-(TETRAHYDRO-2-FURANYLMETHOXY)-9H-PURIN-2- AMINE C10 H13 N5 O2 1h0u P2P N7-(5'-PHOSPHO-ALPHA-RIBOSYL)-2-HYDROXYPURINE C10 H13 N4 O8 P1 1jhr P5P PURINE RIBOSIDE-5'-MONOPHOSPHATE C10 H13 N4 O7 P1 1rbn PPZ 2-(PYRIDO[1,2-E]PURIN-4-YL)AMINO-ETHANOL 2(C11 H11 N5 O1) 1i5v PRH 6-HYDROXY-1,6-DIHYDRO PURINE NUCLEOSIDE 4(C10 H15 N4 O5) 1a4m PRN PURINE 2'-DEOXYRIBO-5'-MONOPHOSPHATE C10 H13 N4 O6 P1 1cl8 PUR PURINE RIBOSIDE C10 H13 N4 O4 1fkw T6A N-[N-(9-B-D-RIBOFURANOSYLPURIN-6-YL) CARBAMOYL]THREONINE-5'-MONOPHOSPHATE C15 H21 N6 O11 P1 1feq TSX N-[4-(1-ALLYL-3-BUTYL-2,6-DIOXO-2,3,6,7-TETRAHYDRO-1H- PURIN-8-YLMETHYL)-PHENYL]-ACETAMIDE C21 H25 N5 O3 1m51 UN4 5-{[(2-AMINO-9H-PURIN-6-YL)OXY]METHYL}-2- PYRROLIDINONE C10 H12 N6 O2 1h0v may be, it is easier for all "non standard" nucleic acids to parse the HETNAM record just as I did and determine dynamically whether there is an additional group to add to the sets nucleic purine pyrimidine T U C A I G Just a low priority remark. Regards, Jan -- Snail to:Jan Reichert, IMB, D-07708 Jena, POB 100813. Voice:+49 3641 6562-05 (Fax:+49 3641 6562-10) :/i mailto:[EMAIL PROTECTED] ------------------------------------------------------- This SF.net email is sponsored by: SF.net Giveback Program. Does SourceForge.net help you be more productive? Does it help you create better code? SHARE THE LOVE, and help us help YOU! Click Here: http://sourceforge.net/donate/ _______________________________________________ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
