Structure of PDB 3aca Chain A Binding Site BS04

Receptor Information

>3aca Chain A (length=196) Species: 9606 (Homo sapiens)

GKQYIISEELISEGKWVKLEKTTYMDPTGKTRTWESVKRTTRKEQTADGV
AVIPVLQRTLHYECIVLVKQFRPPMGGYCIEFPAGLIDDGETPEAAALRE
LEEETGYKGDIAECSPAVCMDPGLSNCTIHIVTVTINGDDAENARPKPKP
GDGEFVEVISLPKNDLLQRLDALVAEEHLTVDARVYSYALALKHAN

Ligand information

• Ligand ID: 8DD
• InChI: InChI=1S/C10H15N5O10P2/c11-8-7-9(13-3-12-8)15(10(17)14-7)6-1-4(16)5(24-6)2-23-27(21,22)25-26(18,19)20/h3-6,16H,1-2H2,(H,14,17)(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,5+,6+/m0/s1
• InChIKey: FEPFWQCDWZFLGY-KVQBGUIXSA-N
• SMILES:
  CACTVS 3.352: Nc1ncnc2N([C@H]3C[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(O)=O)O3)C(=O)Nc12
  OpenEye OEToolkits 1.7.0: c1nc(c2c(n1)N(C(=O)N2)C3CC(C(O3)COP(=O)(O)OP(=O)(O)O)O)N
  OpenEye OEToolkits 1.7.0: c1nc(c2c(n1)N(C(=O)N2)[C@H]3C[C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)N
  CACTVS 3.352: Nc1ncnc2N([CH]3C[CH](O)[CH](CO[P](O)(=O)O[P](O)(O)=O)O3)C(=O)Nc12
• Formula: C10 H15 N5 O10 P2
• Name: 8-oxo-7,8-dihydro-2'-deoxy-adenosine-5'-diphosphate
• ZINC: ZINC000058631723
• PDB chain: 3aca Chain B Residue 209

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3aca Diverse substrate recognition and hydrolysis mechanisms of human NUDT5
• Resolution: 2.05 Å
• Binding residue (original residue number in PDB): W46 E47
• Binding residue (residue number reindexed from 1): W34 E35
• Annotation score: 2

Enzymatic activity

• Enzyme Commision number: 2.7.7.96: ADP-D-ribose pyrophosphorylase.
  3.6.1.13: ADP-ribose diphosphatase.
  3.6.1.58: 8-oxo-dGDP phosphatase.

Gene Ontology

Molecular Function

• GO:0016787 hydrolase activity

External links

• PDB: RCSB:3aca, PDBe:3aca, PDBj:3aca
• PDBsum: 3aca
• PubMed: 21768126
• UniProt: Q9UKK9|NUDT5_HUMAN ADP-sugar pyrophosphatase (Gene Name=NUDT5)