Structure of PDB 4gyz Chain E Binding Site BS01

Receptor Information

>4gyz Chain E (length=249) Species: 10090 (Mus musculus)

STISFITWNIDGLDGCNLPERARGVCSCLALYSPDVVFLQEVIPPYCAYL
KKRAASYTIITGNEEGYFTAILLKKGRVKFKSQEIIPFPNTKMMRNLLCV
NVSLGGNEFCLMTSHLESTREHSAERIRQLKTVLGKMQEAPDSTTVIFAG
DTNLRDQEVIKCGGLPDNVFDAWEFLGKPKHCQYTWDTKANNNLRIPAAY
KHRFDRIFFRAEEGHLIPQSLDLVGLEKLDCGRFPSDHWGLLCTLNVVL

Ligand information

• Ligand ID: D5M
• InChI: InChI=1S/C10H14N5O6P/c11-9-8-10(13-3-12-9)15(4-14-8)7-1-5(16)6(21-7)2-20-22(17,18)19/h3-7,16H,1-2H2,(H2,11,12,13)(H2,17,18,19)/t5-,6+,7+/m0/s1
• InChIKey: KHWCHTKSEGGWEX-RRKCRQDMSA-N
• SMILES:
  CACTVS 3.341: Nc1ncnc2n(cnc12)[CH]3C[CH](O)[CH](CO[P](O)(O)=O)O3
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3CC(C(O3)COP(=O)(O)O)O)N
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O)N
  CACTVS 3.341: Nc1ncnc2n(cnc12)[C@H]3C[C@H](O)[C@@H](CO[P](O)(O)=O)O3
  ACDLabs 10.04: O=P(O)(O)OCC3OC(n2cnc1c(ncnc12)N)CC3O
• Formula: C10 H14 N5 O6 P
• Name: 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
• ChEMBL: CHEMBL1206239
• ZINC: ZINC000001713574
• PDB chain: 4gyz Chain E Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4gyz Mechanism of repair of 5'-topoisomerase II-DNA adducts by mammalian tyrosyl-DNA phosphodiesterase 2.
• Resolution: 2.556 Å
• Binding residue (original residue number in PDB): H236 S239 D272 N274 R276 F325 H359
• Binding residue (residue number reindexed from 1): H115 S118 D151 N153 R155 F204 H238
• Annotation score: 4

Enzymatic activity

• Enzyme Commision number: 3.1.4.-

Gene Ontology

Molecular Function

• GO:0003824 catalytic activity

External links

• PDB: RCSB:4gyz, PDBe:4gyz, PDBj:4gyz
• PDBsum: 4gyz
• PubMed: 23104055
• UniProt: Q9JJX7|TYDP2_MOUSE Tyrosyl-DNA phosphodiesterase 2 (Gene Name=Tdp2)