3L3M | pdb_00003l3m

PARP complexed with A927929


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.275 (Depositor) 
  • R-Value Work: 
    0.202 (Depositor), 0.205 (DCC) 
  • R-Value Observed: 
    0.205 (Depositor) 

Starting Model: other
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Optimization of phenyl-substituted benzimidazole carboxamide poly(ADP-ribose) polymerase inhibitors: identification of (S)-2-(2-fluoro-4-(pyrrolidin-2-yl)phenyl)-1H-benzimidazole-4-carboxamide (A-966492), a highly potent and efficacious inhibitor.

Penning, T.D.Zhu, G.D.Gong, J.Thomas, S.Gandhi, V.B.Liu, X.Shi, Y.Klinghofer, V.Johnson, E.F.Park, C.H.Fry, E.H.Donawho, C.K.Frost, D.J.Buchanan, F.G.Bukofzer, G.T.Rodriguez, L.E.Bontcheva-Diaz, V.Bouska, J.J.Osterling, D.J.Olson, A.M.Marsh, K.C.Luo, Y.Giranda, V.L.

(2010) J Med Chem 53: 3142-3153

  • DOI: https://doi.org/10.1021/jm901775y
  • Primary Citation Related Structures: 
    3L3M

  • PubMed Abstract: 

    We have developed a series of phenylpyrrolidine- and phenylpiperidine-substituted benzimidazole carboxamide poly(ADP-ribose) polymerase (PARP) inhibitors with excellent PARP enzyme potency as well as single-digit nanomolar cellular potency. These efforts led to the identification of (S)-2-(2-fluoro-4-(pyrrolidin-2-yl)phenyl)-1H-benzimidazole-4-carboxamide (22b, A-966492). Compound 22b displayed excellent potency against the PARP-1 enzyme with a K(i) of 1 nM and an EC(50) of 1 nM in a whole cell assay. In addition, 22b is orally bioavailable across multiple species, crosses the blood-brain barrier, and appears to distribute into tumor tissue. It also demonstrated good in vivo efficacy in a B16F10 subcutaneous murine melanoma model in combination with temozolomide and in an MX-1 breast cancer xenograft model both as a single agent and in combination with carboplatin.


  • Organizational Affiliation
    • Cancer Research, Abbott Laboratories 100 Abbott Park Road, Abbott Park, Illinois 60064, USA. thomas.penning@abbott.com

Macromolecule Content 

  • Total Structure Weight: 39.51 kDa 
  • Atom Count: 2,876 
  • Modeled Residue Count: 348 
  • Deposited Residue Count: 350 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Poly [ADP-ribose] polymerase 1350Homo sapiensMutation(s): 1 
Gene Names: PARP1ADPRTPPOL
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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09874
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A92

Query on A92



Download:Ideal Coordinates CCD File
B [auth A]2-{2-fluoro-4-[(2S)-piperidin-2-yl]phenyl}-1H-benzimidazole-7-carboxamide
C19 H19 F N4 O
LGVIXHMVSRYWJL-HNNXBMFYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.275 (Depositor) 
  • R-Value Work:  0.202 (Depositor), 0.205 (DCC) 
  • R-Value Observed: 0.205 (Depositor) 
Space Group: P 3 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.205α = 90
b = 94.205β = 90
c = 68.856γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
CNSrefinement
BUSTERrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2010-06-23 
  • Deposition Author(s): Park, C.H.

Revision History  (Full details and data files)

  • Version 1.0: 2010-06-23
    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