5KPO

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

PDB DOI: https://doi.org/10.2210/pdb5KPO/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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free: 0.303
R-Value Work: 0.238
R-Value Observed: 0.241

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

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.

Macromolecule Content

Total Structure Weight: 79.73 kDa
Atom Count: 5,599
Modelled Residue Count: 701
Deposited Residue Count: 704
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

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 (PDB Primary Data), 2.4.2 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P09874 (Homo sapiens) Explore P09874 Go to UniProtKB: P09874
PHAROS: P09874 GTEx: ENSG00000143799
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P09874
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
6WY Query on 6WY Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	1-[[3-(4-ethyl-3-oxidanylidene-piperazin-1-yl)carbonyl-4-fluoranyl-phenyl]methyl]quinazoline-2,4-dione C₂₂ H₂₁ F N₄ O₄ LGFTWORQFUMEPZ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free: 0.303
R-Value Work: 0.238
R-Value Observed: 0.241
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.34	α = 90
b = 92.36	β = 90
c = 163.44	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2016-12-21

Deposition Author(s):

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

Revision History (Full details and data files)

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.