Structure of PDB 5nyz Chain A Binding Site BS01

Receptor Information
>5nyz Chain A (length=167) Species: 53369 (Dubowvirus dv80alpha) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MTNTLQVKLLSKNARMPERNHKTDAGYDIFSAETVVLEPQEKAVIKTDVA
VSIPEGYVGLLTSRSGVSSKTHLVIETGKIDAGYHGNLGINIKNEHEDDK
MQTIFLRNIDNEKIFEKERHLYKLGSYRIEKGERIAQLVIVPIWTPELKQ
VEEFESVERGEKGFGSS
Ligand information
Ligand IDDUP
InChIInChI=1S/C9H16N3O13P3/c13-5-3-8(12-2-1-7(14)10-9(12)15)24-6(5)4-23-26(16,17)11-27(18,19)25-28(20,21)22/h1-2,5-6,8,13H,3-4H2,(H,10,14,15)(H2,20,21,22)(H3,11,16,17,18,19)/t5-,6+,8+/m0/s1
InChIKeyXZLLMTSKYYYJLH-SHYZEUOFSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C1C(C(OC1N2C=CC(=O)NC2=O)COP(=O)(NP(=O)(O)OP(=O)(O)O)O)O
CACTVS 3.341O[C@H]1C[C@@H](O[C@@H]1CO[P@](O)(=O)N[P@](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O
OpenEye OEToolkits 1.5.0C1[C@@H]([C@H](O[C@H]1N2C=CC(=O)NC2=O)CO[P@](=O)(N[P@@](=O)(O)OP(=O)(O)O)O)O
CACTVS 3.341O[CH]1C[CH](O[CH]1CO[P](O)(=O)N[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)NP(=O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)CC2O
FormulaC9 H16 N3 O13 P3
Name2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE
ChEMBLCHEMBL1232397
DrugBankDB01965
ZINC
PDB chain5nyz Chain A Residue 201 [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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PDB5nyz Dissecting the link between the enzymatic activity and the SaPI inducing capacity of the phage 80 alpha dUTPase.
Resolution2.5 Å
Binding residue
(original residue number in PDB)		G78 I80 D81 Y84 G89
Binding residue
(residue number reindexed from 1)		G78 I80 D81 Y84 G89
Annotation score3
Binding affinityPDBbind-CN: -logKd/Ki=5.03,Kd=9.4uM
Enzymatic activity
Catalytic site (original residue number in PDB) A25 R64 G66 L73 D81
Catalytic site (residue number reindexed from 1) A25 R64 G66 L73 D81
Enzyme Commision number 3.6.1.23: dUTP diphosphatase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0004170 dUTP diphosphatase activity
GO:0016787 hydrolase activity
GO:0046872 metal ion binding
Biological Process
GO:0006226 dUMP biosynthetic process
GO:0046081 dUTP catabolic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5nyz, PDBe:5nyz, PDBj:5nyz
PDBsum5nyz
PubMed28894239
UniProtA4ZF98

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