Structure of PDB 4gv8 Chain A Binding Site BS01

Receptor Information
>4gv8 Chain A (length=153) Species: 12360 (Dubowvirus dv11) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NTLQVRLLSENARMPERNHKTDAGYDIFSAETVVLEPQEKAVIKTDVAVS
IPEGYVGLLTSRSGVSSKTHLVIETGKIDAGYHGNLGINIKNDAIASNGY
ITPGVFDIKGEIDLSDAIRQYGTYQINEGDKLAQLVIVPIWTPELKQVEE
FES
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 chain4gv8 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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PDB4gv8 Structure and enzymatic mechanism of a moonlighting dUTPase
Resolution2.1 Å
Binding residue
(original residue number in PDB)		G78 I80 D81 Y84 G89
Binding residue
(residue number reindexed from 1)		G76 I78 D79 Y82 G87
Annotation score3
Binding affinityMOAD: Kd=0.32uM
PDBbind-CN: -logKd/Ki=6.49,Kd=0.32uM
Enzymatic activity
Catalytic site (original residue number in PDB) A25 R64 G66 L73 D81
Catalytic site (residue number reindexed from 1) A23 R62 G64 L71 D79
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:4gv8, PDBe:4gv8, PDBj:4gv8
PDBsum4gv8
PubMed24311572
UniProtQ8SDV3

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