5J3S

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.254 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

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, L.E., Bartlett, E.J., Brissett, N.C., Raoof, A., Watson, M., Jordan, A.M., Ogilvie, D.J., Ward, S.E., Atack, J.R., Pearl, L.H., Caldecott, K.W., Oliver, A.W.

(2016) Biochem.J. 473: 1869-1879

  • DOI: 10.1042/BCJ20160180
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Tyrosyl-DNA phosphodiesterase 2 (TDP2) is a 5'-tyrosyl DNA phosphodiesterase important for the repair of DNA adducts generated by non-productive (abortive) activity of topoisomerase II (TOP2). TDP2 facilitates therapeutic resistance to topoisomerase ...

    Tyrosyl-DNA phosphodiesterase 2 (TDP2) is a 5'-tyrosyl DNA phosphodiesterase important for the repair of DNA adducts generated by non-productive (abortive) activity of topoisomerase II (TOP2). TDP2 facilitates therapeutic resistance to topoisomerase poisons, which are widely used in the treatment of a range of cancer types. Consequently, TDP2 is an interesting target for the development of small molecule inhibitors that could restore sensitivity to topoisomerase-directed therapies. Previous studies identified a class of deazaflavin-based molecules that showed inhibitory activity against TDP2 at therapeutically useful concentrations, but their mode of action was uncertain. We have confirmed that the deazaflavin series inhibits TDP2 enzyme activity in a fluorescence-based assay, suitable for high-throughput screen (HTS)-screening. We have gone on to determine crystal structures of these compounds bound to a 'humanized' form of murine TDP2. The structures reveal their novel mode of action as competitive ligands for the binding site of an incoming DNA substrate, and point the way to generating novel and potent inhibitors of TDP2.

    Organizational Affiliation: 

    Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer BN1 9RQ, U.K. Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer BN1 9RQ, U.K.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tyrosyl-DNA phosphodiesterase 2
A
253Homo sapiensMutation(s): 1 
Gene Names: TDP2 (EAP2, TTRAP)
EC: 3.1.4.-
Find proteins for O95551 (Homo sapiens)
Go to Gene View: TDP2
Go to UniProtKB:  O95551
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6FQ
Query on 6FQ
Download SDF File 
Download CCD File 
A
2,4-dioxo-10-[3-(1H-tetrazol-5-yl)phenyl]-2,3,4,10-tetrahydropyrimido[4,5-b]quinoline-8-carbonitrile
C19 H10 N8 O2
NDVGJTJBERLSGL-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
6FQIC50: 590 nM (99) BINDINGDB
6FQEC50: 40 nM (99) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.254 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 68.516α = 90.00
b = 68.516β = 90.00
c = 209.505γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
PHASERphasing
Aimlessdata scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-05-04
    Type: Initial release
  • Version 1.1: 2016-07-06
    Type: Database references