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Table 1 Naming convention statistics for selected ligands

From: Wanted: unique names for unique atom positions. PDB-wide analysis of diastereotopic atom names of small molecules containing diphosphate

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 B1) 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
  1. # = number of PDB files in which the given naming convention was observed.
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BMC Bioinformatics

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