Structure of PDB 4ndf Chain B Binding Site BS03

Receptor Information

>4ndf Chain B (length=180) Species: 9606 (Homo sapiens)

GSHMGHWSQGLKISMQDPKMQVYKDEQVVVIKDKYPKARYHWLVLPWTSI
SSLKAVAREHLELLKHMHTVGEKVIVDFAGSSKLRFRLGYHAIPSMSHVH
LHVISQDFDSPCLKNKKHWNSFNTEYFLESQAVIEMVQEAGRVTVRDGMP
ELLKLPLRCHECQQLLPSIPQLKEHLRKHW

Ligand information

• Ligand ID: AMP
• InChI: InChI=1S/C10H14N5O7P/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(22-10)1-21-23(18,19)20/h2-4,6-7,10,16-17H,1H2,(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
• InChIKey: UDMBCSSLTHHNCD-KQYNXXCUSA-N
• SMILES:
  CACTVS 3.370: Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O
  CACTVS 3.370: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O
  OpenEye OEToolkits 1.7.6: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N
  ACDLabs 12.01: O=P(O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
  OpenEye OEToolkits 1.7.6: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)O)O)O)N
• Formula: C10 H14 N5 O7 P
• Name: ADENOSINE MONOPHOSPHATE
• ChEMBL: CHEMBL752
• DrugBank: DB00131
• ZINC: ZINC000003860156
• PDB chain: 4ndf Chain B Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4ndf Aprataxin resolves adenylated RNA-DNA junctions to maintain genome integrity.
• Resolution: 1.944 Å
• Binding residue (original residue number in PDB): L171 D193 K194 Y195 L203 H251 S255 M256 H260 H262
• Binding residue (residue number reindexed from 1): L11 D33 K34 Y35 L43 H91 S95 M96 H100 H102
• Annotation score: 5

Enzymatic activity

• Enzyme Commision number: 3.6.1.71: adenosine-5'-diphospho-5'-[DNA] diphosphatase.
  3.6.1.72: DNA-3'-diphospho-5'-guanosine diphosphatase.

Gene Ontology

Molecular Function

• GO:0003824 catalytic activity

External links

• PDB: RCSB:4ndf, PDBe:4ndf, PDBj:4ndf
• PDBsum: 4ndf
• PubMed: 24362567
• UniProt: Q7Z2E3|APTX_HUMAN Aprataxin (Gene Name=APTX)