5KPO | pdb_00005kpo

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 (Depositor), 0.301 (DCC)
R-Value Work:
0.238 (Depositor), 0.239 (DCC)
R-Value Observed:
0.241 (Depositor)

wwPDB Validation 3D Report Full Report

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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
Modeled Residue Count: 701
Deposited Residue Count: 704
Unique protein chains: 1

Macromolecules

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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
6WY	BindingDB: 5KPO	IC50: 7.6 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free: 0.303 (Depositor), 0.301 (DCC)
R-Value Work: 0.238 (Depositor), 0.239 (DCC)
R-Value Observed: 0.241 (Depositor)

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

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Ligand Structure Quality Assessment

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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

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.