Structure of PDB 3of3 Chain B Binding Site BS02

Receptor Information
>3of3 Chain B (length=240) Species: 666 (Vibrio cholerae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ATPHINAQMGDFADVVLMPGDPLRAKYIAENFLDNAVQVCDVRNMFGYTG
TYKGRKISVMGHGMGIPSCSIYVTELIKDYGVKKIIRVGSCGAVNEGIKV
RDVVIGMGACTDSKVNRIRFKDHDFAAIADYKMVKAAEEAAKARGIDVKV
GNLFSAELFYTPDPSMFDVMDKYGIVGVEMEAAGIYGVAAEYGAKALAIC
TVSDHIKTGEQTTSEERQNTFNEMIEIALDSVLIGDQAGY
Ligand information
Ligand IDDIH
InChIInChI=1S/C12H16N4O3/c17-5-8-3-16(4-9(8)18)2-7-1-13-11-10(7)14-6-15-12(11)19/h1,6,8-9,13,17-18H,2-5H2,(H,14,15,19)/p+1/t8-,9+/m1/s1
InChIKeyAFNHHLILYQEHKK-BDAKNGLRSA-O
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6c1c(c2c([nH]1)C(=O)NC=N2)C[NH+]3CC(C(C3)O)CO
OpenEye OEToolkits 2.0.6c1c(c2c([nH]1)C(=O)NC=N2)C[NH+]3C[C@@H]([C@H](C3)O)CO
CACTVS 3.385OC[CH]1C[NH+](C[CH]1O)Cc2c[nH]c3C(=O)NC=Nc23
CACTVS 3.385OC[C@H]1C[NH+](C[C@@H]1O)Cc2c[nH]c3C(=O)NC=Nc23
FormulaC12 H17 N4 O3
Name7-[[(3R,4R)-3-(hydroxymethyl)-4-oxidanyl-pyrrolidin-1-ium-1-yl]methyl]-3,5-dihydropyrrolo[3,2-d]pyrimidin-4-one
ChEMBL
DrugBank
ZINC
PDB chain3of3 Chain E Residue 500 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB3of3 Crystal structure of PNP with an inhibitor DADME_immH from Vibrio cholerae
Resolution1.83 Å
Binding residue
(original residue number in PDB)		H18 R57
Binding residue
(residue number reindexed from 1)		H4 R43
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) H18 G34 R38 R57 E89 R101 S104 S217 D218 I220 R231
Catalytic site (residue number reindexed from 1) H4 G20 R24 R43 E75 R87 S90 S203 D204 I206 R217
Enzyme Commision number 2.4.2.1: purine-nucleoside phosphorylase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0004731 purine-nucleoside phosphorylase activity
GO:0016757 glycosyltransferase activity
GO:0016763 pentosyltransferase activity
Biological Process
GO:0006139 nucleobase-containing compound metabolic process
GO:0006152 purine nucleoside catabolic process
GO:0009116 nucleoside metabolic process
GO:0009164 nucleoside catabolic process
GO:0042278 purine nucleoside metabolic process
Cellular Component
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3of3, PDBe:3of3, PDBj:3of3
PDBsum3of3
PubMed
UniProtQ9KPM0|DEOD1_VIBCH Purine nucleoside phosphorylase DeoD-type 1 (Gene Name=deoD1)

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