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


Ligand Structure Quality Assessment 


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:  
    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) ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Biotin carboxylaseA, B486Escherichia coli K-12Mutation(s): 0 
Gene Names: accCfabGb3256JW3224
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24182
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
JZK
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
DGENNQRBHYDWGG-UHFFFAOYSA-N
 Ligand Interaction
CO3
Query on CO3

Download Ideal Coordinates CCD File 
C [auth A]CARBONATE ION
C O3
BVKZGUZCCUSVTD-UHFFFAOYSA-L
 Ligand Interaction
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

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

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

  • Deposited Date: 2009-09-23 
  • 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