3GJW

PARP complexed with A968427

• PDB DOI: https://doi.org/10.2210/pdb3GJW/pdb

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


• Deposited: 2009-03-09 Released: 2010-03-09 
• Deposition Author(s): Park, C.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.276 
• R-Value Work: 0.209 
• R-Value Observed: 0.212 

Starting Model: experimental

Literature

Synthesis and SAR of novel tricyclic quinoxalinone inhibitors of poly(ADP-ribose)polymerase-1 (PARP-1)

Miyashiro, J., Woods, K.W., Park, C.H., Liu, X., Shi, Y., Johnson, E.F., Bouska, J.J., Olson, A.M., Luo, Y., Fry, E.H., Giranda, V.L., Penning, T.D.

(2009) Bioorg Med Chem Lett 19: 4050-4054

• PubMed: 19553114 
• DOI: https://doi.org/10.1016/j.bmcl.2009.06.016
• Primary Citation of Related Structures:  
  3GJW


• PubMed Abstract: 
  

  Based on screening hit 1, a series of tricyclic quinoxalinones have been designed and evaluated for inhibition of PARP-1. Substitutions at the 7- and 8-positions of the quinoxalinone ring led to a number of compounds with good enzymatic and cellular potency. The tricyclic quinoxalinone class is sensitive to modifications of both the amine substituent and the tricyclic core. The synthesis and structure-activity relationship studies are presented.

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Organizational Affiliation: 

Cancer Research, GPRD, Abbott Laboratories, 100 Abbott Park Rd., Abbott Park, IL 60064, USA. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 39.44 kDa 
• Atom Count: 2,899 
• Modelled Residue Count: 350 
• Deposited Residue Count: 350 
• Unique protein chains: 1

Macromolecules

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 (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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GJW	B [auth A]	7-(pyrrolidin-1-ylmethyl)pyrrolo[1,2-a]quinoxalin-4(5H)-one C16 H17 N3 O ZLYVTQGSZRQZLA-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
GJW	BindingDB:  3GJW	Ki: 5 (nM) from 1 assay(s)
		EC50: 6 (nM) from 1 assay(s)
	PDBBind:  3GJW	Ki: 5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.276 
• R-Value Work: 0.209 
• R-Value Observed: 0.212 
• Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.644	α = 90
b = 93.644	β = 90
c = 68.89	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

Entry History 

Deposition Data

• Released Date: 2010-03-09 
Deposition Author(s): Park, C.H.

Revision History  

• Version 1.0: 2010-03-09
  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