Structure of PDB 4oop Chain B Binding Site BS03

Receptor Information
>4oop Chain B (length=142) Species: 3702 (Arabidopsis thaliana) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PSPFFKVKKLSEKAVIPTRGSPLSAGYDLSSAVDSKVPARGKALIPTDLS
IAVPEGTYARIAPRSGLAWKHSIDVGAGVIDADYRGPVGVILFNHSDADF
EVKFGDRIAQLIIEKIVTPDVVEVDDLDETVRGDGGFGSTGV
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 chain4oop Chain B Residue 203 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4oop Structural insights into the mechanism defining substrate affinity in Arabidopsis thaliana dUTPase: the role of tryptophan 93 in ligand orientation.
Resolution1.5 Å
Binding residue
(original residue number in PDB)		R156 G160 F161 G162 S163 T164
Binding residue
(residue number reindexed from 1)		R132 G136 F137 G138 S139 T140
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) A49 R88 G90 I97 D105
Catalytic site (residue number reindexed from 1) A25 R64 G66 I73 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:0042802 identical protein binding
GO:0046872 metal ion binding
Biological Process
GO:0006226 dUMP biosynthetic process
GO:0006281 DNA repair
GO:0009117 nucleotide metabolic process
GO:0046081 dUTP catabolic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4oop, PDBe:4oop, PDBj:4oop
PDBsum4oop
PubMed26666293
UniProtQ9STG6|DUT_ARATH Deoxyuridine 5'-triphosphate nucleotidohydrolase (Gene Name=DUT)

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