Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

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

Macromolecule Content

• Total Structure Weight: 39507.19 
• Atom Count: 2760 
• 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): 1 


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

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.5 Å
• R-Value Free: 0.275 
• R-Value Work: 0.202 

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


• 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. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Poly [ADP-ribose] polymerase 1	A	350	Homo sapiens	Mutation(s): 1  Gene Names: PARP1 (ADPRT, PPOL) EC: 2.4.2.30
Find proteins for P09874 (Homo sapiens) Go to Gene View: PARP1 Go to UniProtKB:  P09874

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
A92	A	2-{2-fluoro-4-[(2S)-piperidin-2-yl]phenyl}-1H-benzimidazole-7-carboxamide C19 H19 F N4 O LGVIXHMVSRYWJL-HNNXBMFYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
A92	Ki: 6 nM BINDINGMOAD
A92	Ki: 6 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.5 Å
• R-Value Free: 0.275 
• R-Value Work: 0.202 
• Space Group: P 3 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 94.205	α = 90.00
b = 94.205	β = 90.00
c = 68.856	γ = 120.00

Software Package:

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

Structure Validation

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
  Type: Version format compliance