Structure of PDB 4dk4 Chain A Binding Site BS04

Receptor Information

>4dk4 Chain A (length=218) Species: 5691 (Trypanosoma brucei)

SLSPLILRSLAELQDGLNTVVDKNWRQLRRPGDWSLAITMEAAELLDSYP
WKWWKNVKAQPDLQNVKIELTDILHFSLSGAMQVSADFMFFPLSDTNNAL
ASFQNIIRLASLQRFQLVTSAVIAAADDIGFNLVAYYVAKHTLNGIRQMK
GYKDGTYVKVQKGVEDNELLHGCISPFSLDDVTNEGNYKTKWDDIMHRVY
DAFGTPKEERLNIGHWLK

Ligand information

• Ligand ID: DUN
• InChI: InChI=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
• InChIKey: COFNIXBQVWFHTR-SHYZEUOFSA-N
• SMILES:
  CACTVS 3.341: O[CH]1C[CH](O[CH]1CO[P](O)(=O)N[P](O)(O)=O)N2C=CC(=O)NC2=O
  OpenEye OEToolkits 1.5.0: C1C(C(OC1N2C=CC(=O)NC2=O)COP(=O)(NP(=O)(O)O)O)O
  OpenEye OEToolkits 1.5.0: C1[C@@H]([C@H](O[C@H]1N2C=CC(=O)NC2=O)CO[P@@](=O)(NP(=O)(O)O)O)O
  ACDLabs 10.04: O=P(O)(O)NP(=O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)CC2O
  CACTVS 3.341: O[C@H]1C[C@@H](O[C@@H]1CO[P@@](O)(=O)N[P](O)(O)=O)N2C=CC(=O)NC2=O
• Formula: C9 H15 N3 O10 P2
• Name: 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-DIPHOSPHATE;
  2,4(1H,3H)-PYRIMIDINEDIONE;
  1-[2-DEOXY-5-O-[HYDROXY(PHOSPHONOAMINO)PHOSPHINYL]-BETA-D-ERYTHRO-PENTOFURANOSYL]-
• DrugBank: DB03641
• PDB chain: 4dk4 Chain B Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4dk4 On the catalytic mechanism of dimeric dUTPases.
• Resolution: 1.9 Å
• Binding residue (original residue number in PDB): K59 W60 W61
• Binding residue (residue number reindexed from 1): K52 W53 W54
• Annotation score: 2

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

External links

• PDB: RCSB:4dk4, PDBe:4dk4, PDBj:4dk4
• PDBsum: 4dk4
• PubMed: 24001052
• UniProt: Q57ZH3