3GN7

PARP complexed with A861696

PDB DOI: https://doi.org/10.2210/pdb3GN7/pdb

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

Deposited: 2009-03-16 Released: 2010-03-16
Deposition Author(s): Park, C.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.271
R-Value Work: 0.194

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

PARP complexed with A861696

Park, C.H.

To be published.

Macromolecule Content

Total Structure Weight: 39.41 kDa
Atom Count: 2,879
Modelled Residue Count: 350
Deposited Residue Count: 350
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Poly [ADP-ribose] polymerase 1	A	350	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
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
3GN Query on 3GN Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	2-[(2S)-2-methylpyrrolidin-2-yl]-1H-benzimidazole-7-carboxamide C₁₃ H₁₆ N₄ O JNAHVYVRKWKWKQ-ZDUSSCGKSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
3GN	BindingDB: 3GN7	Ki: min: 4, max: 5 (nM) from 2 assay(s)
3GN	PDBBind: 3GN7	Ki: 5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.271
R-Value Work: 0.194
Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.349	α = 90
b = 94.349	β = 90
c = 68.204	γ = 120

Software Package:

Software Name	Purpose
BUSTER-TNT	refinement
CNS	refinement
CNX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing
HKL-2000	data collection

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-03-16

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-03-16
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2019-07-24
Changes: Data collection, Refinement description
Version 1.3: 2021-10-20
Changes: Database references, Derived calculations
Version 1.4: 2023-09-06
Changes: Data collection, Refinement description

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.