› 5j3s

X-ray diffraction
3.4Å resolution

Crystal structure of the catalytic domain of human tyrosyl DNA phosphodiesterase 2 in complex with a small molecule inhibitor

Released:
DOI: 10.2210/pdb5j3s/pdb
PDB entry 5j3s coloured by chain, front view.
PDB entry 5j3s coloured by chain, side view.
PDB entry 5j3s coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Mode of action of DNA-competitive small molecule inhibitors of tyrosyl DNA phosphodiesterase 2.
Hornyak P, Askwith T, Walker S, Komulainen E, Paradowski M, Pennicott LE, Bartlett EJ, Brissett NC, Raoof A, Watson M, Jordan AM, Ogilvie DJ, Ward SE, Atack JR, Pearl LH, Caldecott KW, Oliver AW
OpenAccess logo Biochem J 473 1869-79 (2016)
PMID: 27099339

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-131947 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Tyrosyl-DNA phosphodiesterase 2 Chain: A
Molecule details ›
Chain: A
Length: 253 amino acids
Theoretical weight: 28.82 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O95551 (Residues: 113-362; Coverage: 69%)
Gene names: AD-022, EAP2, TDP2, TTRAP
Sequence domains: Endonuclease/Exonuclease/phosphatase family
Structure domains: Endonuclease/exonuclease/phosphatase

Ligands and Environments

1 bound ligand:
Ligand 6FQ 1 x 6FQ
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04
Spacegroup: P6522
Unit cell:
a: 68.516Å b: 68.516Å c: 209.505Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.255 0.254 0.273
Expression system: Escherichia coli

Quick links

Citations

4 review citations

Recent developments in topoisomerase-targeted cancer chemotherapy.
Hevener et al. (2018)
3 more

5 mentions without citation

Synthesis and Biological Evaluation of the First Triple Inhibitors of Human Topoisomerase 1, Tyrosyl-DNA Phosphodiesterase 1 (Tdp1), and Tyrosyl-DNA Phosphodiesterase 2 (Tdp2).
Wang et al. (2017)
4 more