beta-ketoacyl-ACP synthase I (KAS) from E. coli with bound amino- thiazole inhibitor

Experimental Data Snapshot

  • Resolution: 1.36 Å
  • R-Value Free: 0.151 
  • R-Value Work: 0.119 
  • R-Value Observed: 0.121 

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This is version 1.4 of the entry. See complete history


Structure-Assisted Discovery of an Aminothiazole Derivative as a Lead Molecule for Inhibition of Bacterial Fatty-Acid Synthesis.

Pappenberger, G.Schulz-Gasch, T.Kusznir, E.Mueller, F.Hennig, M.

(2007) Acta Crystallogr D Biol Crystallogr 63: 1208

  • DOI: https://doi.org/10.1107/S0907444907049852
  • Primary Citation of Related Structures:  
    2VB7, 2VB8, 2VB9, 2VBA

  • PubMed Abstract: 

    Fatty-acid synthesis in bacteria is of great interest as a target for the discovery of antibacterial compounds. The addition of a new acetyl moiety to the growing fatty-acid chain, an essential step in this process, is catalyzed by beta-ketoacyl-ACP synthase (KAS). It is inhibited by natural antibiotics such as cerulenin and thiolactomycin; however, these lack the requirements for optimal drug development. Structure-based biophysical screening revealed a novel synthetic small molecule, 2-phenylamino-4-methyl-5-acetylthiazole, that binds to Escherichia coli KAS I with a binding constant of 25 microM as determined by fluorescence titration. A 1.35 A crystal structure of its complex with its target reveals noncovalent interactions with the active-site Cys163 and hydrophobic residues of the fatty-acid binding pocket. The active site is accessible through an open conformation of the Phe392 side chain and no conformational changes are induced at the active site upon ligand binding. This represents a novel binding mode that differs from thiolactomycin or cerulenin interaction. The structural information on the protein-ligand interaction offers strategies for further optimization of this low-molecular-weight compound.

  • Organizational Affiliation

    F. Hoffmann-La Roche Ltd, Pharma Research Discovery, CH-4070 Basel, Switzerland.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D
406Escherichia coliMutation(s): 0 
Find proteins for P0A953 (Escherichia coli (strain K12))
Explore P0A953 
Go to UniProtKB:  P0A953
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A953
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on P4T

Download Ideal Coordinates CCD File 
C12 H12 N2 O S
Binding Affinity Annotations 
IDSourceBinding Affinity
P4T PDBBind:  2VBA Kd: 2.50e+4 (nM) from 1 assay(s)
Binding MOAD:  2VBA Kd: 2.50e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.36 Å
  • R-Value Free: 0.151 
  • R-Value Work: 0.119 
  • R-Value Observed: 0.121 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.95α = 90
b = 139.48β = 90
c = 212.17γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-12-25
    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: 2019-05-08
    Changes: Data collection, Experimental preparation, Other
  • Version 1.4: 2023-12-13
    Changes: Data collection, Database references, Other, Refinement description