Structure of PDB 5f9k Chain B Binding Site BS04

Receptor Information
>5f9k Chain B (length=130) Species: 44689 (Dictyostelium discoideum) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GSHMFKVKKLSDKAIIPQRGSKGAAGYDLSSAHELVVPAHGKALAMTDLQ
IAIPDGTYGRIAPRSGLAWKNFIDCGAGVIDSDYRGNVGVVLFNHSDVDF
KVAVGDRVAQLIFERIVTPEPLEVDEIDET
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 chain5f9k Chain C Residue 203 [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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PDB5f9k Mitochondrial localization of Dictyostelium discoideum dUTPase mediated by its N-terminus.
Resolution2.179 Å
Binding residue
(original residue number in PDB)		A77 G78 V79 I80 Y84 G89
Binding residue
(residue number reindexed from 1)		A77 G78 V79 I80 Y84 G89
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) A25 R64 G66 I73 D81
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
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:5f9k, PDBe:5f9k, PDBj:5f9k
PDBsum5f9k
PubMed31910901
UniProtQ54BW5|DUT_DICDI Deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial (Gene Name=dut)

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