Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 29.21 kDa 
• Atom Count: 1761 
• Modelled Residue Count: 236 
• Deposited Residue Count: 253 
• Unique protein chains: 1

5J3S

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

• PDB DOI: 10.2210/pdb5J3S/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2016-03-31 Released: 2016-05-04 
• Deposition Author(s): Hornyak, P., Pearl, L.H., Caldecott, K.W., Oliver, A.W.

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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 

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

• PubMed: 27099339 
• DOI: 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosyl-DNA phosphodiesterase 2	A	253	Homo sapiens	Mutation(s): 1  Gene Names: TDP2, EAP2, TTRAP, AD-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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6FQ	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
ID	Source	Binding 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 = 68.516	α = 90
b = 68.516	β = 90
c = 209.505	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2016-03-31 
• Released Date: 2016-05-04 
Deposition Author(s): Hornyak, P., Pearl, L.H., Caldecott, K.W., Oliver, A.W.

Revision History  

• 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