2VB8

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.151 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 

Literature

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.,Sect.D 63: 1208

  • DOI: 10.1107/S0907444907049852
  • Primary Citation of Related Structures:  

  • 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 ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE 1
A, B, C, D
406Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: fabB (fabC)
EC: 2.3.1.41
Find proteins for P0A953 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A953
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TLM
Query on TLM
Download SDF File 
Download CCD File 
A, B, C, D
THIOLACTOMYCIN
4-HYDROXY-3,5-DIMETHYL-5-(2-METHYL-BUTA-1,3-DIENYL)-5H-THIOPHEN-2-ONE
C11 H14 O2 S
SYQNUQSGEWNWKV-XUIVZRPNSA-N
 Ligand Interaction
CL
Query on CL
Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
TLMIC50: 12000 nM (100) BINDINGDB
TLMKd: 25000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.151 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 59.139α = 90.00
b = 138.345β = 90.00
c = 211.968γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
REFMACrefinement
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-12-25
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2019-05-08
    Type: Data collection, Experimental preparation, Other