Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 107.47 kDa 
• Atom Count: 6942 
• Modelled Residue Count: 827 
• Deposited Residue Count: 972 
• Unique protein chains: 1

3JZF

Crystal structure of biotin carboxylase from E. Coli in complex with benzimidazoles series

• PDB DOI: 10.2210/pdb3JZF/pdb

• Classification: LIGASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-09-23 Released: 2009-11-03 
• Deposition Author(s): Orth, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.13 Å
• R-Value Free: 0.236 
• R-Value Work: 0.203 

Literature

Discovery and optimization of antibacterial AccC inhibitors.

Cheng, C.C., Shipps, G.W., Yang, Z., Sun, B., Kawahata, N., Soucy, K.A., Soriano, A., Orth, P., Xiao, L., Mann, P., Black, T.

(2009) Bioorg Med Chem Lett 19: 6507-6514

• PubMed: 19875284 
• DOI: 10.1016/j.bmcl.2009.10.057
• Primary Citation of Related Structures:  
  3JZF, 3JZI


• PubMed Abstract: 
  

The biotin carboxylase (AccC) is part of the multi-component bacterial acetyl coenzyme-A carboxylase (ACCase) and is essential for pathogen survival. We describe herein the affinity optimization of an initial hit to give 2-(2-chlorobenzylamino)-1-(cyclohexylmethyl)-1H-benzo[d]imidazole-5-carboxamide (1), which was identified using our proprietary Automated Ligand Identification System (ALIS).(1) The X-ray co-crystal structure of 1 was solved and revealed several key interactions and opportunities for further optimization in the ATP site of AccC. Structure Based Drug Design (SBDD) and parallel synthetic approaches resulted in a novel series of AccC inhibitors, exemplified by (R)-2-(2-chlorobenzylamino)-1-(2,3-dihydro-1H-inden-1-yl)-1H-imidazo[4,5-b]pyridine-5-carboxamide (40). This compound is a potent and selective inhibitor of bacterial AccC with an IC(50) of 20 nM and a MIC of 0.8 microg/mL against a sensitized strain of Escherichia coli (HS294 E. coli).

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Organizational Affiliation: 

Schering-Plough Research Institute, Cambridge, MA 02141, United States. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Biotin carboxylase	A, B	486	Escherichia coli K-12	Mutation(s): 0  Gene Names: accC, fabG, b3256, JW3224 EC: 6.3.4.14 (PDB Primary Data), 6.4.1.2 (PDB Primary Data)
UniProt
Find proteins for P24182 (Escherichia coli (strain K12)) Explore P24182  Go to UniProtKB:  P24182

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
JZK	D [auth B]	2-[(2-chlorobenzyl)amino]-1-(cyclohexylmethyl)-1H-benzimidazole-5-carboxamide C22 H25 Cl N4 O DGENNQRBHYDWGG-UHFFFAOYSA-N
CO3	C [auth A]	CARBONATE ION C O3 BVKZGUZCCUSVTD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
JZK	PDBBind:  3JZF	IC50: 5000 (nM) from 1 assay(s)
	Binding MOAD:  3JZF	IC50: 5000 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.13 Å
• R-Value Free: 0.236 
• R-Value Work: 0.203 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.37	α = 90
b = 107.514	β = 90
c = 122.345	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
AMoRE	phasing
BUSTER	refinement
DENZO	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-09-23 
• Released Date: 2009-11-03 
Deposition Author(s): Orth, P.

Revision History  

• Version 1.0: 2009-11-03
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance