5KPN

Structure of human PARP1 catalytic domain bound to a quinazoline-2,4(1H,3H)-dione inhibitor

• PDB DOI: https://doi.org/10.2210/pdb5KPN/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2016-07-05 Released: 2016-12-21 
• Deposition Author(s): Cao, R., Wang, Y.L., Zhou, J., Yao, H.P., Huang, N., Xu, B.L.
• Funding Organization(s): Special Funds for National Public Benefit Research Institute

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.293 
• R-Value Work: 0.233 
• R-Value Observed: 0.236 

Literature

Structure of human PARP1 catalytic domain bound to a quinazoline-2,4(1H,3H)-dione inhibitor

Cao, R., Wang, Y.L., Zhou, J., Yao, H.P., Huang, N., Xu, B.L.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 79.75 kDa 
• Atom Count: 5,601 
• Modelled Residue Count: 701 
• Deposited Residue Count: 704 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Poly [ADP-ribose] polymerase 1	A, B	352	Homo sapiens	Mutation(s): 1  Gene Names: PARP1, ADPRT, PPOL EC: 2.4.2.30
UniProt & NIH Common Fund Data Resources
Find proteins for P09874 (Homo sapiens) Explore P09874  Go to UniProtKB:  P09874
PHAROS:  P09874 GTEx:  ENSG00000143799

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6WX	C [auth A], D [auth B]	1-[[4-fluoranyl-3-(3-oxidanylidene-4-propyl-piperazin-1-yl)carbonyl-phenyl]methyl]quinazoline-2,4-dione C23 H23 F N4 O4 JJDFDZDTXGPNIC-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.293 
• R-Value Work: 0.233 
• R-Value Observed: 0.236 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.43	α = 90
b = 92.37	β = 90
c = 164.01	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-12-21 
Deposition Author(s): Cao, R., Wang, Y.L., Zhou, J., Yao, H.P., Huang, N., Xu, B.L.

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Funding Organization	Location	Grant Number
Special Funds for National Public Benefit Research Institute	China	2013CHX16

Revision History  

• Version 1.0: 2016-12-21
  Type: Initial release
  
• Version 1.1: 2024-03-20
  Changes: Data collection, Database references