2W70

Crystal structure of Biotin carboxylase from E. coli in complex with the amino-thiazole-pyrimidine fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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: 10.1021/cb9000102
  • Primary Citation of Related Structures:  
    2W6Z, 2W6Q, 2W6M, 2W6N, 2W6O, 2W70, 2W6P, 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 discover ...

    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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
BIOTIN CARBOXYLASEAB449Escherichia coliMutation(s): 0 
EC: 6.3.4.14 (PDB Primary Data), 6.4.1.2 (PDB Primary Data)
Find proteins for P24182 (Escherichia coli (strain K12))
Explore P24182 
Go to UniProtKB:  P24182
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
L22
Query on L22

Download CCD File 
A, B
4-(2-amino-1,3-thiazol-4-yl)pyrimidin-2-amine
C7 H7 N5 S
FHERIFNAOMUFRM-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
L22IC50:  12000   nM  BindingDB
L22IC50:  12000   nM  Binding MOAD
L22IC50 :  12000   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.234α = 90
b = 106.215β = 90
c = 122.635γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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