Biological Assembly 1  

 3D View: Structure | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 39.51 kDa 
• Atom Count: 2876 
• Modelled Residue Count: 348 
• Deposited Residue Count: 350 
• Unique protein chains: 1

3L3M

PARP complexed with A927929

• DOI: 10.2210/pdb3L3M/pdb

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


• Deposited: 2009-12-17 Released: 2010-06-23 
• Deposition Author(s): Park, C.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.275 
• R-Value Work: 0.202 
• R-Value Observed: 0.205 

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

• PubMed: 20337371 
• DOI: 10.1021/jm901775y
• Primary Citation of 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.

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Organizational Affiliation: 

Cancer Research, Abbott Laboratories 100 Abbott Park Road, Abbott Park, Illinois 60064, USA. [e-mail]

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
A92 (Subject of Investigation/LOI)	B [auth A]	2-{2-fluoro-4-[(2S)-piperidin-2-yl]phenyl}-1H-benzimidazole-7-carboxamide C19 H19 F N4 O LGVIXHMVSRYWJL-HNNXBMFYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
A92	Binding MOAD:  3L3M	Ki: 6 (nM) from 1 assay(s)
	PDBBind:  3L3M	Ki: 6 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.275 
• R-Value Work: 0.202 
• R-Value Observed: 0.205 
• Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.205	α = 90
b = 94.205	β = 90
c = 68.856	γ = 120

Software Package:

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

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 2009-12-17 
• Released Date: 2010-06-23 
Deposition Author(s): Park, C.H.

Revision History  

• 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