Structure of PDB 3f4f Chain B Binding Site BS02

Receptor Information
>3f4f Chain B (length=138) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DKVLKIQLRSASATVPTKGSATAAGYDIYASQDITIPAMGQGMVSTDISF
TVPVGTYGRIAPRSGLAVKNGIQTGAGVVDRDYTGEVKVVLFNHSQRDFA
IKKGDRVAQLILEKIVDDAQIVVVDSLEESARGAGGFG
Ligand information
Ligand IDUMP
InChIInChI=1S/C9H13N2O8P/c12-5-3-8(11-2-1-7(13)10-9(11)14)19-6(5)4-18-20(15,16)17/h1-2,5-6,8,12H,3-4H2,(H,10,13,14)(H2,15,16,17)/t5-,6+,8+/m0/s1
InChIKeyJSRLJPSBLDHEIO-SHYZEUOFSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=P(O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)CC2O
CACTVS 3.370O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O
OpenEye OEToolkits 1.7.6C1[C@@H]([C@H](O[C@H]1N2C=CC(=O)NC2=O)COP(=O)(O)O)O
CACTVS 3.370O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O
OpenEye OEToolkits 1.7.6C1C(C(OC1N2C=CC(=O)NC2=O)COP(=O)(O)O)O
FormulaC9 H13 N2 O8 P
Name2'-DEOXYURIDINE 5'-MONOPHOSPHATE;
DUMP
ChEMBLCHEMBL211312
DrugBankDB03800
ZINCZINC000004228260
PDB chain3f4f Chain B Residue 200 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB3f4f Structure and activity of the Saccharomyces cerevisiae dUTP pyrophosphatase DUT1, an essential housekeeping enzyme.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		I65 A81 G82 V83 D85 Y88 K93
Binding residue
(residue number reindexed from 1)		I60 A76 G77 V78 D80 Y83 K88
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) G24 A29 Y31 R68 G70 I77 D85
Catalytic site (residue number reindexed from 1) G19 A24 Y26 R63 G65 I72 D80
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:0035870 dITP diphosphatase activity
GO:0046872 metal ion binding
Biological Process
GO:0006226 dUMP biosynthetic process
GO:0009117 nucleotide metabolic process
GO:0009213 pyrimidine deoxyribonucleoside triphosphate catabolic process
GO:0035863 dITP catabolic process
GO:0046081 dUTP catabolic process
Cellular Component
GO:0005634 nucleus
GO:0005737 cytoplasm

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3f4f, PDBe:3f4f, PDBj:3f4f
PDBsum3f4f
PubMed21548881
UniProtP33317|DUT_YEAST Deoxyuridine 5'-triphosphate nucleotidohydrolase (Gene Name=DUT1)

[Back to BioLiP]