PARP complexed with A906894

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.214 

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Ligand Structure Quality Assessment 

This is version 1.4 of the entry. See complete history


Discovery and SAR of substituted 3-oxoisoindoline-4-carboxamides as potent inhibitors of poly(ADP-ribose) polymerase (PARP) for the treatment of cancer.

Gandhi, V.B.Luo, Y.Liu, X.Shi, Y.Klinghofer, V.Johnson, E.F.Park, C.Giranda, V.L.Penning, T.D.Zhu, G.D.

(2010) Bioorg Med Chem Lett 20: 1023-1026

  • DOI: https://doi.org/10.1016/j.bmcl.2009.12.042
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Through conformational restriction of a benzamide by formation of a seven-membered hydrogen-bond with an oxindole carbonyl group, a series of PARP inhibitors was designed for appropriate orientation for binding to the PARP surface. This series of compounds with a 3-oxoisoindoline-4-carboxamide core structure, displayed modest to good activity against PARP-1 in both intrinsic and cellular assays. SAR studies at the lactam nitrogen of the pharmacophore have suggested that a secondary or tertiary amine is important for cellular potency. An X-ray structure of compound 1e bound to the protein confirmed the formation of a seven-membered intramolecular hydrogen bond. Though revealed previously in peptides, this type of seven-membered intramolecular hydrogen bond is rarely observed in small molecules. Largely due to the formation of the intramolecular hydrogen bond, the 3-oxoisoindoline-4-carboxamide core structure appears to be planar in the X-ray structure. An additional hydrogen bond interaction of the piperidine nitrogen to Gly-888 also contributes to the binding affinity of 1e to PARP-1.

  • Organizational Affiliation

    Cancer Research, GPRD, Abbott Laboratories, 100 Abbott Park Road, Abbott Park, IL 60064, USA. viraj.b.gandhi@abbott.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Poly [ADP-ribose] polymerase 1350Homo sapiensMutation(s): 1 
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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09874
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on L3L

Download Ideal Coordinates CCD File 
B [auth A]3-oxo-2-piperidin-4-yl-2,3-dihydro-1H-isoindole-4-carboxamide
C14 H17 N3 O2
Binding Affinity Annotations 
IDSourceBinding Affinity
L3L BindingDB:  3L3L Ki: 33 (nM) from 1 assay(s)
EC50: 51 (nM) from 1 assay(s)
PDBBind:  3L3L Ki: 33 (nM) from 1 assay(s)
Binding MOAD:  3L3L Ki: 33 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.214 
  • Space Group: P 3 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.023α = 90
b = 94.023β = 90
c = 68.773γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

  • Released Date: 2010-12-22 
  • Deposition Author(s): Park, C.H.

Revision History  (Full details and data files)

  • Version 1.0: 2010-12-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-10-13
    Changes: Database references, Derived calculations
  • Version 1.3: 2024-02-21
    Changes: Data collection
  • Version 1.4: 2024-04-03
    Changes: Refinement description