6W7L | pdb_00006w7l

Structure of Tdp1 catalytic domain in complex with inhibitor XZ632p

• PDB DOI: https://doi.org/10.2210/pdb6W7L/pdb

• Classification: HYDROLASE/HYDROLASE Inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-03-19 Released: 2021-03-24 
• Deposition Author(s): Lountos, G.T., Zhao, X.Z., Kiselev, E., Tropea, J.E., Needle, D., Pommier, Y., Burke, T.R., Waugh, D.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 
  0.219 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.183 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

Small molecule microarray identifies inhibitors of tyrosyl-DNA phosphodiesterase 1 that simultaneously access the catalytic pocket and two substrate binding sites

Zhao, X.Z., Kiselev, E., Lountos, G.T., Wang, W., Tropea, J.E., Needle, D., Hilimire, T.A., Schneekloth, J.S., Waugh, D.S., Pommier, Y., Burke, T.R.

(2021) Chemical Science 12: 3876-3884

• DOI: https://doi.org/10.1039/D0SC05411A

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 105.25 kDa 
• Atom Count: 7,846 
• Modeled Residue Count: 873 
• Deposited Residue Count: 922 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosyl-DNA phosphodiesterase 1	A, B	461	Homo sapiens	Mutation(s): 0  Gene Names: TDP1 EC: 3.1.4
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NUW8 (Homo sapiens) Explore Q9NUW8  Go to UniProtKB:  Q9NUW8
PHAROS:  Q9NUW8 GTEx:  ENSG00000042088

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TGV (Subject of Investigation/LOI)	C [auth A], E [auth B]	4-[(2-phenylimidazo[1,2-a]pyrazin-3-yl)amino]benzene-1,2-dicarboxylic acid C20 H14 N4 O4 DQITWSHGMZMNEP-UHFFFAOYSA-N
EDO	D [auth A], F [auth B], G [auth B], H [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free:  0.219 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.183 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.032	α = 90
b = 105.817	β = 90
c = 194.211	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-03-24 
Deposition Author(s): Lountos, G.T., Zhao, X.Z., Kiselev, E., Tropea, J.E., Needle, D., Pommier, Y., Burke, T.R., Waugh, D.S.

Revision History  

• Version 1.0: 2021-03-24
  Type: Initial release
  
• Version 1.1: 2021-03-31
  Changes: Database references
• Version 1.2: 2023-10-18
  Changes: Data collection, Database references, Refinement description