Structure of PDB 3epw Chain B Binding Site BS02

Receptor Information
>3epw Chain B (length=326) Species: 5699 (Trypanosoma vivax) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AKNVVLDHDGNLDDFVAMVLLASNTEKVRLIGALCTDADCFVENGFNVTG
KIMCLMHNNMNLPLFPIGKSAATAVNPFPKEWRCLAKNMDDMPILNIPEN
VELWDKIKAENEKYEGQQLLADLVMNSEEKVTICVTGPLSNVAWCIDKYG
EKFTSKVEECVIMGGAVDVRGNVFLPSTDGTAEWNIYWDPASAKTVFGCP
GLRRIMFSLDSTNTVPVRSPYVQRFGEQTNFLLSILVGTMWAMCTHCELL
RDGDGYYAWDALTAAYVVDQKVANVDPVPIDVVVDKQPNEGATVRTDAEN
YPLTFVARNPEAEFFLDMLLRSARAC
Ligand information
Ligand IDJMQ
InChIInChI=1S/C12H16N4O4/c17-4-7-11(19)8(18)3-16(7)2-6-1-13-10-9(6)14-5-15-12(10)20/h1,5,7-8,11,13,17-19H,2-4H2,(H,14,15,20)/t7-,8+,11-/m1/s1
InChIKeyOKGGSJRJIFFOGK-VHSKPIJISA-N
SMILES
SoftwareSMILES
CACTVS 3.370OC[C@@H]1[C@@H](O)[C@@H](O)CN1Cc2c[nH]c3C(=O)NC=Nc23
ACDLabs 12.01O=C2NC=Nc1c(cnc12)CN3C(C(O)C(O)C3)CO
OpenEye OEToolkits 1.7.0c1c(c2c([nH]1)C(=O)NC=N2)CN3CC(C(C3CO)O)O
OpenEye OEToolkits 1.7.0c1c(c2c([nH]1)C(=O)NC=N2)C[N@]3C[C@@H]([C@@H]([C@H]3CO)O)O
CACTVS 3.370OC[CH]1[CH](O)[CH](O)CN1Cc2c[nH]c3C(=O)NC=Nc23
FormulaC12 H16 N4 O4
Name7-(((2R,3R,4S)-3,4-dihydroxy-2-(hydroxymethyl)pyrrolidin-1-yl)methyl)-3H-pyrrolo[3,2-d]pyrimidin-4(5H)-one
ChEMBLCHEMBL493456
DrugBank
ZINCZINC000038878792
PDB chain3epw Chain B Residue 1003 [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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PDB3epw Crystal structures of T. vivax nucleoside hydrolase in complex with new potent and specific inhibitors.
Resolution1.3 Å
Binding residue
(original residue number in PDB)		N12 D14 D40 F79 W83 M164 N173 E184 N186 R252 Y257 W260 D261
Binding residue
(residue number reindexed from 1)		N11 D13 D39 F78 W82 M163 N172 E183 N185 R251 Y256 W259 D260
Annotation score1
Binding affinityMOAD: Ki=4.4nM
Enzymatic activity
Catalytic site (original residue number in PDB) D10 D15 D40 W83 T137 W185 N186 W260 D261
Catalytic site (residue number reindexed from 1) D9 D14 D39 W82 T136 W184 N185 W259 D260
Enzyme Commision number 3.2.2.1: purine nucleosidase.
Gene Ontology
Molecular Function
GO:0016798 hydrolase activity, acting on glycosyl bonds
GO:0016799 hydrolase activity, hydrolyzing N-glycosyl compounds
GO:0046872 metal ion binding
Biological Process
GO:0006139 nucleobase-containing compound metabolic process

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Molecular Function
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Biological Process
External links
PDB RCSB:3epw, PDBe:3epw, PDBj:3epw
PDBsum3epw
PubMed19281874
UniProtQ9GPQ4

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