3JZF

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

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

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

  • DOI: 10.1016/j.bmcl.2009.10.057
  • Primary Citation of Related Structures:  

  • 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-(cy ...

    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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Biotin carboxylase
A, B
486Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: accC (fabG)
EC: 6.3.4.14
Find proteins for P24182 (Escherichia coli (strain K12))
Go to UniProtKB:  P24182
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
JZK
Query on JZK
Download SDF File 
Download CCD File 
B
2-[(2-chlorobenzyl)amino]-1-(cyclohexylmethyl)-1H-benzimidazole-5-carboxamide
C22 H25 Cl N4 O
DGENNQRBHYDWGG-UHFFFAOYSA-N
 Ligand Interaction
CO3
Query on CO3
Download SDF File 
Download CCD File 
A
CARBONATE ION
C O3
BVKZGUZCCUSVTD-UHFFFAOYSA-L
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
JZKIC50: 5000 nM BINDINGMOAD
JZKIC50: 5000 nM PDBBIND
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 = 84.370α = 90.00
b = 107.514β = 90.00
c = 122.345γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
BUSTERrefinement
CrystalCleardata collection
HKL-2000data scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

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
    Type: Version format compliance