4BNV

Crystal structure of 3-oxoacyl-(acyl-carrier-protein) reductase (FabG) from Pseudomonas aeruginosa in complex with 1-(2-chlorophenyl)-3-(1- methylbenzimidazol-2-yl)urea at 2.5A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Discovery of an Allosteric Inhibitor Binding Site in Resolution

Cukier, C.D.Hope, A.Elamin, A.Moynie, L.Schnell, R.Schach, S.Kneuper, H.Singh, M.Naismith, J.Lindqvist, Y.Gray, D.Schneider, G.

(2013) Acs Chem.Biol. 8: 2518

  • DOI: 10.1021/cb4005063
  • Primary Citation of Related Structures:  4AG3, 4BNU, 4BNW, 4BNX, 4BNY, 4BO0, 4BO1, 4BO2, 4BO3, 4BO5, 4BO7, 4BO8, 4BO9, 4AFN, 4BNT, 4BNZ, 4BO4, 4BO6

  • PubMed Abstract: 
  • 3-Oxo-acyl-acyl carrier protein (ACP) reductase (FabG) plays a key role in the bacterial fatty acid synthesis II system in pathogenic microorganisms, which has been recognized as a potential drug target. FabG catalyzes reduction of a 3-oxo-acyl-ACP i ...

    3-Oxo-acyl-acyl carrier protein (ACP) reductase (FabG) plays a key role in the bacterial fatty acid synthesis II system in pathogenic microorganisms, which has been recognized as a potential drug target. FabG catalyzes reduction of a 3-oxo-acyl-ACP intermediate during the elongation cycle of fatty acid biosynthesis. Here, we report gene deletion experiments that support the essentiality of this gene in P. aeruginosa and the identification of a number of small molecule FabG inhibitors with IC50 values in the nanomolar to low micromolar range and good physicochemical properties. Structural characterization of 16 FabG-inhibitor complexes by X-ray crystallography revealed that the compounds bind at a novel allosteric site located at the FabG subunit-subunit interface. Inhibitor binding relies primarily on hydrophobic interactions, but specific hydrogen bonds are also observed. Importantly, the binding cavity is formed upon complex formation and therefore would not be recognized by virtual screening approaches. The structure analysis further reveals that the inhibitors act by inducing conformational changes that propagate to the active site, resulting in a displacement of the catalytic triad and the inability to bind NADPH.


    Organizational Affiliation

    Department of Medical Biochemistry and Biophysics, Karolinska Institutet , 17177 Stockholm, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
3-OXOACYL-[ACYL-CARRIER-PROTEIN] REDUCTASE FABG
A, B, C, D
269Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228)Gene Names: fabG
EC: 1.1.1.100
Find proteins for O54438 (Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228))
Go to UniProtKB:  O54438
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
Q7U
Query on Q7U

Download SDF File 
Download CCD File 
B, D
1-(2-chlorophenyl)-3-(1-methylbenzimidazol-2-yl)urea
C15 H13 Cl N4 O
NOFMBQDHIIQTMR-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
Q7UIC50: 30 nM BINDINGMOAD
Q7UIC50: 30 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.204 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 53.860α = 90.00
b = 108.070β = 90.00
c = 146.610γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
PHASERphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-09-18
    Type: Initial release
  • Version 1.1: 2013-11-27
    Type: Database references
  • Version 1.2: 2017-09-13
    Type: Data collection