3L3L

PARP complexed with A906894


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

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: 10.1016/j.bmcl.2009.12.042
  • Primary Citation of Related Structures:  
    3L3L

  • 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 com ...

    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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Poly [ADP-ribose] polymerase 1A350Homo sapiensMutation(s): 1 
Gene Names: PARP1ADPRTPPOL
EC: 2.4.2.30 (PDB Primary Data), 2.4.2 (UniProt)
Find proteins for P09874 (Homo sapiens)
Explore P09874 
Go to UniProtKB:  P09874
NIH Common Fund Data Resources
PHAROS  P09874
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
L3L
Query on L3L

Download CCD File 
A
3-oxo-2-piperidin-4-yl-2,3-dihydro-1H-isoindole-4-carboxamide
C14 H17 N3 O2
KISOFIKBJFDVKM-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
L3LKi :  33   nM  PDBBind
L3LKi:  33   nM  Binding MOAD
L3LEC50:  51   nM  BindingDB
L3LKi:  33   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
CNSrefinement
BUSTERrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2009-12-17 
  • Released Date: 2010-12-22 
  • Deposition Author(s): Park, C.H.

Revision History 

  • Version 1.0: 2010-12-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance