2W6O

Crystal structure of Biotin carboxylase from E. coli in complex with 4-Amino-7,7-dimethyl-7,8-dihydro-quinazolinone fragment

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.230 

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:  

  • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BIOTIN CARBOXYLASE
A, C
449Escherichia 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
OA3
Query on OA3
Download SDF File 
Download CCD File 
A, C
4-amino-7,7-dimethyl-7,8-dihydroquinazolin-5(6H)-one
C10 H13 N3 O
DYPFWRCGECJCBK-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL
Download SDF File 
Download CCD File 
A, C
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
OA3IC50: 60800 nM (100) BINDINGDB
OA3IC50: 60800 nM BINDINGMOAD
OA3IC50: 60800 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.230 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 68.629α = 90.00
b = 113.367β = 90.00
c = 121.737γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data reduction
MOLREPphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-05-19
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance