2W6P

Crystal structure of Biotin carboxylase from E. coli in complex with 5-Methyl-6-phenyl-quinazoline-2,4-diamine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.188 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 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: 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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ACETYL-COA CARBOXYLASE
A, B
449Escherichia coliMutation(s): 0 
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
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OA4
Query on OA4

Download Ideal Coordinates CCD File 
C [auth A]5-methyl-6-phenylquinazoline-2,4-diamine
C15 H14 N4
HUCOXWPHDFINIW-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
OA4 PDBBind:  2W6P IC50: 333 (nM) from 1 assay(s)
BindingDB:  2W6P IC50: 333 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.188 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.986α = 90
b = 106.475β = 90
c = 121.978γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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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