Structure of PDB 4xba Chain B Binding Site BS01

Receptor Information

>4xba Chain B (length=193) Species: 284812 (Schizosaccharomyces pombe 972h-)

SFRDNLKVYIESPESYKNVIYYDDDVVLVRDMFPKSKMHLLLMTRDPHLT
HVHPLEIMMKHRSLVEKLVSYVQGDLSGLIFDEARNCLSQQLTNEALCNY
IKVGFHAGPSMNNLHLHIMTLDHVSPSLKNSAHYISFTSPFFVKIDTPTS
NLPTLFQEDLKCWRCGETFGRHFTKLKAHLQEEYDDWLDKSVS

Ligand information

• Ligand ID: 5GP
• InChI: InChI=1S/C10H14N5O8P/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(23-9)1-22-24(19,20)21/h2-3,5-6,9,16-17H,1H2,(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
• InChIKey: RQFCJASXJCIDSX-UUOKFMHZSA-N
• SMILES:
  CACTVS 3.341: NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O
  CACTVS 3.341: NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O
  ACDLabs 10.04: O=C1c2ncn(c2N=C(N)N1)C3OC(C(O)C3O)COP(=O)(O)O
  OpenEye OEToolkits 1.5.0: c1nc2c(n1C3C(C(C(O3)COP(=O)(O)O)O)O)N=C(NC2=O)N
  OpenEye OEToolkits 1.5.0: c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N=C(NC2=O)N
• Formula: C10 H14 N5 O8 P
• Name: GUANOSINE-5'-MONOPHOSPHATE
• ChEMBL: CHEMBL283807
• DrugBank: DB01972
• ZINC: ZINC000002159505
• PDB chain: 4xba Chain B Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4xba DNA3'pp5'G de-capping activity of aprataxin: effect of cap nucleoside analogs and structural basis for guanosine recognition.
• Resolution: 1.5 Å
• Binding residue (original residue number in PDB): L38 Y41 D63 M64 F65 H138 S142 M143 H147 H149
• Binding residue (residue number reindexed from 1): L6 Y9 D31 M32 F33 H106 S110 M111 H115 H117
• Annotation score: 4

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:4xba, PDBe:4xba, PDBj:4xba
• PDBsum: 4xba
• PubMed: 26007660
• UniProt: O74859|APTX_SCHPO Aprataxin-like protein (Gene Name=hnt3)