Primary Citation PubMed: 9618487
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Wanted: unique names for unique atom positions. PDB-wide analysis of diastereotopic atom names of small molecules containing diphosphate.
(2008) BMC Bioinformatics 9 Suppl 9
PubMed: 18793461 | PubMedCentral: PMC2537567 | DOI: 10.1186/1471-2105-9-S9-S16
Table 1 Naming convention statistics for selected ligands ligand code ligand name center atom pro -S pro -R # bias (%) example PDB ACO acetyl-coenzyme A P1A O1A O2A 22 42% 1DM3 O2A O1A 30 58% 1B87 P2A... O4A O5A 25 48% 1B87 O5A O4A 27 52% 1DM3 ADP adenosine-5'-diphosphate PA O1A O2A 211 33% 1A6E O2A O1A 419 67% 13PK ATP adenosine-5'-triphosphate PA O1A O2A 103 30% 1B0U O2A O1A 240 70% 1A0I COA coenzyme A P1A O1A O2A 67 45% 1ACA O2A O1A 81 55% 1CM0 P2A O4A O5A 67 46% 1ESM O5A O4A 78 54% 1ACA CTP cytidine-5'-triphosphate PA O1A O2A 20 49% 1GQ9 O2A O1A 21 51% 1COZ FAD flavin-adenine dinucleotide P O1P O2P 554 87% 1A8P O2P O1P 81 13% 1B2R PA O1A O2A 290 46% 1AHV O2A O1A 345 54% 1A8P GTP guanosine-5'-triphosphate PA O1A O2A 35 36% 1CKM O2A O1A 62 64% 1A8R NAD nicotinamide-adenine-dinucleotide PA O1A O2A 144 27% 1A5Z O2A O1A 388 73% 1A4Z PN O1N O2N 394 74% 1A4Z O2N O1N 135 26% 1A7A NAP nadp nicotinamide-adenine-dinucleotide phosphate PA O1A O2A 87 26% 1CIV O2A O1A 247 74% 1A27 PN O1N O2N 280 83% 1A27 O2N O1N 58 17% 1A80 TPP thiamine diphosphate (i.e. vitamin B 1 ) PA O1A O2A 25 56% 1AY0 O2A O1A 20 44% 1B0P UDP uridine-5'-diphosphate PA O1A O2A 80 79% 1BGU O2A O1A 21 21% 1C3J # = number of PDB files in which the given naming convention was observed.
Publication Year: 2008
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