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: 3.40 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.254 
  • R-Value Observed: 0.255 

Starting Model: experimental
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This is version 1.3 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: https://doi.org/10.1042/BCJ20160180
  • Primary Citation of Related Structures:  
    5J3P, 5J3S, 5J3Z, 5J42

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosyl-DNA phosphodiesterase 2253Homo sapiensMutation(s): 1 
Gene Names: TDP2EAP2TTRAPAD-022
EC: 3.1.4
UniProt & NIH Common Fund Data Resources
Find proteins for O95551 (Homo sapiens)
Explore O95551 
Go to UniProtKB:  O95551
PHAROS:  O95551
GTEx:  ENSG00000111802 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO95551
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6FQ
Query on 6FQ

Download Ideal Coordinates CCD File 
B [auth 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
Binding Affinity Annotations 
IDSourceBinding Affinity
6FQ BindingDB:  5J3S IC50: min: 41, max: 590 (nM) from 2 assay(s)
EC50: 40 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.254 
  • R-Value Observed: 0.255 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.516α = 90
b = 68.516β = 90
c = 209.505γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-05-04
    Type: Initial release
  • Version 1.1: 2016-07-06
    Changes: Database references
  • Version 1.2: 2019-10-16
    Changes: Data collection
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Refinement description