3UIC

Crystal Structure of FabI, an Enoyl Reductase from F. tularensis, in complex with a Novel and Potent Inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.241 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural and enzymatic analyses reveal the binding mode of a novel series of Francisella tularensis enoyl reductase (FabI) inhibitors.

Mehboob, S.Hevener, K.E.Truong, K.Boci, T.Santarsiero, B.D.Johnson, M.E.

(2012) J.Med.Chem. 55: 5933-5941

  • DOI: 10.1021/jm300489v

  • PubMed Abstract: 
  • Because of structural and mechanistic differences between eukaryotic and prokaryotic fatty acid synthesis enzymes, the bacterial pathway, FAS-II, is an attractive target for the design of antimicrobial agents. We have previously reported the identifi ...

    Because of structural and mechanistic differences between eukaryotic and prokaryotic fatty acid synthesis enzymes, the bacterial pathway, FAS-II, is an attractive target for the design of antimicrobial agents. We have previously reported the identification of a novel series of benzimidazole compounds with particularly good antibacterial effect against Francisella tularensis, a Category A biowarfare pathogen. Herein we report the crystal structure of the F. tularensis FabI enzyme in complex with our most active benzimidazole compound bound with NADH. The structure reveals that the benzimidazole compounds bind to the substrate site in a unique conformation that is distinct from the binding motif of other known FabI inhibitors. Detailed inhibition kinetics have confirmed that the compounds possess a novel inhibitory mechanism that is unique among known FabI inhibitors. These studies could have a strong impact on future antimicrobial design efforts and may reveal new avenues for the design of FAS-II active antibacterial compounds.


    Organizational Affiliation

    Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, 900 S. Ashland Avenue, Chicago, Illinois 60607-7173, United States. mjohnson@uic.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Enoyl-[acyl-carrier-protein] reductase [NADH]
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
280Francisella tularensis subsp. tularensis (strain SCHU S4 / Schu 4)Mutation(s): 0 
Gene Names: fabI
EC: 1.3.1.9
Find proteins for Q5NGQ3 (Francisella tularensis subsp. tularensis (strain SCHU S4 / Schu 4))
Go to UniProtKB:  Q5NGQ3
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
09T
Query on 09T

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
1-(3,4-dichlorobenzyl)-5,6-dimethyl-1H-benzimidazole
C16 H14 Cl2 N2
PCJBTWVYIQBUCM-UHFFFAOYSA-N
 Ligand Interaction
NAD
Query on NAD

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
09TKi: 360 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.241 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 85.410α = 90.00
b = 123.461β = 90.02
c = 203.330γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
XDSdata reduction
HKL-2000data collection
REFMACrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-06-06
    Type: Initial release
  • Version 1.1: 2013-02-06
    Type: Database references