Structure of PDB 4dk4 Chain A Binding Site BS01

Receptor Information
>4dk4 Chain A (length=218) Species: 5691 (Trypanosoma brucei) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SLSPLILRSLAELQDGLNTVVDKNWRQLRRPGDWSLAITMEAAELLDSYP
WKWWKNVKAQPDLQNVKIELTDILHFSLSGAMQVSADFMFFPLSDTNNAL
ASFQNIIRLASLQRFQLVTSAVIAAADDIGFNLVAYYVAKHTLNGIRQMK
GYKDGTYVKVQKGVEDNELLHGCISPFSLDDVTNEGNYKTKWDDIMHRVY
DAFGTPKEERLNIGHWLK
Ligand information
Ligand IDDUN
InChIInChI=1S/C9H15N3O10P2/c13-5-3-8(12-2-1-7(14)10-9(12)15)22-6(5)4-21-24(19,20)11-23(16,17)18/h1-2,5-6,8,13H,3-4H2,(H,10,14,15)(H4,11,16,17,18,19,20)/t5-,6+,8+/m0/s1
InChIKeyCOFNIXBQVWFHTR-SHYZEUOFSA-N
SMILES
SoftwareSMILES
CACTVS 3.341O[CH]1C[CH](O[CH]1CO[P](O)(=O)N[P](O)(O)=O)N2C=CC(=O)NC2=O
OpenEye OEToolkits 1.5.0C1C(C(OC1N2C=CC(=O)NC2=O)COP(=O)(NP(=O)(O)O)O)O
OpenEye OEToolkits 1.5.0C1[C@@H]([C@H](O[C@H]1N2C=CC(=O)NC2=O)CO[P@@](=O)(NP(=O)(O)O)O)O
ACDLabs 10.04O=P(O)(O)NP(=O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)CC2O
CACTVS 3.341O[C@H]1C[C@@H](O[C@@H]1CO[P@@](O)(=O)N[P](O)(O)=O)N2C=CC(=O)NC2=O
FormulaC9 H15 N3 O10 P2
Name2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-DIPHOSPHATE;
2,4(1H,3H)-PYRIMIDINEDIONE;
1-[2-DEOXY-5-O-[HYDROXY(PHOSPHONOAMINO)PHOSPHINYL]-BETA-D-ERYTHRO-PENTOFURANOSYL]-
ChEMBL
DrugBankDB03641
ZINC
PDB chain4dk4 Chain A Residue 301 [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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PDB4dk4 On the catalytic mechanism of dimeric dUTPases.
Resolution1.9 Å
Binding residue
(original residue number in PDB)
N25 E48 D79 H82 F83 K208 N212 R215 Y220 K227
Binding residue
(residue number reindexed from 1)
N18 E41 D72 H75 F76 K140 N144 R147 Y152 K159
Annotation score2
Enzymatic activity
Enzyme Commision number 3.6.1.23: dUTP diphosphatase.
Gene Ontology
Molecular Function
GO:0004170 dUTP diphosphatase activity
GO:0016787 hydrolase activity
GO:0046872 metal ion binding
Cellular Component
GO:0005654 nucleoplasm
GO:0005829 cytosol

View graph for
Molecular Function

View graph for
Cellular Component
External links
PDB RCSB:4dk4, PDBe:4dk4, PDBj:4dk4
PDBsum4dk4
PubMed24001052
UniProtQ57ZH3

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