5KPP | pdb_00005kpp

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

PDB DOI: https://doi.org/10.2210/pdb5KPP/pdb

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

Deposited: 2016-07-05 Released: 2016-11-30
Deposition Author(s): Cao, R., Wang, Y.L., Zhou, J., Huang, N., Xu, B.L.
Funding Organization(s): Special Funds for National Public Benefit Research Institute

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.33 Å
R-Value Free:
0.284 (Depositor), 0.280 (DCC)
R-Value Work:
0.239 (Depositor), 0.240 (DCC)
R-Value Observed:
0.241 (Depositor)

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., Huang, N., Xu, B.L.

To be published.

Macromolecule Content

Total Structure Weight: 79.29 kDa
Atom Count: 5,752
Modeled Residue Count: 698
Deposited Residue Count: 700
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	350	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
6WZ Query on 6WZ Download Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	1-[[4-fluoranyl-3-[(3R)-3-methyl-4-[2,2,2-tris(fluoranyl)ethyl]piperazin-1-yl]carbonyl-phenyl]methyl]quinazoline-2,4-dione C₂₃ H₂₂ F₄ N₄ O₃ WJSBPAZKQYZPAE-CQSZACIVSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
6WZ	BindingDB: 5KPP	IC50: 16 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.33 Å
R-Value Free: 0.284 (Depositor), 0.280 (DCC)
R-Value Work: 0.239 (Depositor), 0.240 (DCC)
R-Value Observed: 0.241 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.656	α = 90
b = 92.691	β = 90
c = 163.487	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: 2016-11-30

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: 2016-11-30
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.