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

Experimental Data Snapshot

  • Resolution: 2.13 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.203 

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This is version 1.2 of the entry. See complete history


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

  • DOI: https://doi.org/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).

  • Organizational Affiliation

    Schering-Plough Research Institute, Cambridge, MA 02141, United States. cccheng@alum.mit.edu

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Biotin carboxylase
A, B
486Escherichia coli K-12Mutation(s): 0 
Gene Names: accCfabGb3256JW3224
EC: (PDB Primary Data), (PDB Primary Data)
Find proteins for P24182 (Escherichia coli (strain K12))
Explore P24182 
Go to UniProtKB:  P24182
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24182
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on JZK

Download Ideal Coordinates CCD File 
D [auth B]2-[(2-chlorobenzyl)amino]-1-(cyclohexylmethyl)-1H-benzimidazole-5-carboxamide
C22 H25 Cl N4 O
Query on CO3

Download Ideal Coordinates CCD File 
C O3
Binding Affinity Annotations 
IDSourceBinding 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

  • 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 = 84.37α = 90
b = 107.514β = 90
c = 122.345γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
DENZOdata reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2009-11-03
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description