Crystal structure of Biotin carboxylase from E. coli in complex with the 3-(3-Methyl-but-2-enyl)-3H-purin-6-ylamine fragment

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.186 

wwPDB Validation 

Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


Discovery of Antibacterial Biotin Carboxylase Inhibitors by Virtual Screening and Fragment-Based Approaches.

Mochalkin, I.Miller, J.R.Narasimhan, L.S.Thanabal, V.Erdman, P.Cox, P.Prasad, J.V.Lightle, S.Huband, M.Stover, K.

(2009) ACS Chem Biol 4: 473

  • DOI: https://doi.org/10.1021/cb9000102
  • Primary Citation of Related Structures:  
    2W6M, 2W6N, 2W6O, 2W6P, 2W6Q, 2W6Z, 2W70, 2W71

  • PubMed Abstract: 

    As part of our effort to inhibit bacterial fatty acid biosynthesis through the recently validated target biotin carboxylase, we employed a unique combination of two emergent lead discovery strategies. We used both de novo fragment-based drug discovery and virtual screening, which employs 3D shape and electrostatic property similarity searching. We screened a collection of unbiased low-molecular-weight molecules and identified a structurally diverse collection of weak-binding but ligand-efficient fragments as potential building blocks for biotin carboxylase ATP-competitive inhibitors. Through iterative cycles of structure-based drug design relying on successive fragment costructures, we improved the potency of the initial hits by up to 3000-fold while maintaining their ligand-efficiency and desirable physicochemical properties. In one example, hit-expansion efforts resulted in a series of amino-oxazoles with antibacterial activity. These results successfully demonstrate that virtual screening approaches can substantially augment fragment-based screening approaches to identify novel antibacterial agents.

  • Organizational Affiliation

    Pfizer, Inc., Michigan Laboratories, Ann Arbor, Michigan 48105, USA. Igor_Mochalkin@yahoo.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
449Escherichia coliMutation(s): 0 
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
Binding Affinity Annotations 
IDSourceBinding Affinity
L21 PDBBind:  2W6Z IC50: 1.50e+6 (nM) from 1 assay(s)
BindingDB:  2W6Z IC50: 1.50e+6 (nM) from 1 assay(s)
Binding MOAD:  2W6Z IC50: 1.50e+6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.186 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.482α = 90
b = 106.895β = 90
c = 122.413γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-05-19
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description