4CV3

Crystal structure of E. coli FabI in complex with NADH and PT166


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Rational Design of Broad Spectrum Antibacterial Activity Based on a Clinically Relevant Enoyl-Acyl Carrier Protein (Acp) Reductase Inhibitor.

Schiebel, J.Chang, A.Shah, S.Lu, Y.Liu, L.Pan, P.Hirschbeck, M.W.Tareilus, M.Eltschkner, S.Yu, W.Cummings, J.E.Knudson, S.E.Bommineni, G.R.Walker, S.G.Slayden, R.A.Sotriffer, C.A.Tonge, P.J.Kisker, C.

(2014) J.Biol.Chem. 289: 15987

  • DOI: 10.1074/jbc.M113.532804
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Determining the molecular basis for target selectivity is of particular importance in drug discovery. The ideal antibiotic should be active against a broad spectrum of pathogenic organisms with a minimal effect on human targets. CG400549, a Staphyloc ...

    Determining the molecular basis for target selectivity is of particular importance in drug discovery. The ideal antibiotic should be active against a broad spectrum of pathogenic organisms with a minimal effect on human targets. CG400549, a Staphylococcus-specific 2-pyridone compound that inhibits the enoyl-acyl carrier protein reductase (FabI), has recently been shown to possess human efficacy for the treatment of methicillin-resistant Staphylococcus aureus infections, which constitute a serious threat to human health. In this study, we solved the structures of three different FabI homologues in complex with several pyridone inhibitors, including CG400549. Based on these structures, we rationalize the 65-fold reduced affinity of CG400549 toward Escherichia coli versus S. aureus FabI and implement concepts to improve the spectrum of antibacterial activity. The identification of different conformational states along the reaction coordinate of the enzymatic hydride transfer provides an elegant visual depiction of the relationship between catalysis and inhibition, which facilitates rational inhibitor design. Ultimately, we developed the novel 4-pyridone-based FabI inhibitor PT166 that retained favorable pharmacokinetics and efficacy in a mouse model of S. aureus infection with extended activity against Gram-negative and mycobacterial organisms.


    Organizational Affiliation

    the Institute of Pharmacy and Food Chemistry, University of Wuerzburg, Am Hubland, D-97074 Wuerzburg, Germany.,the Institute for Chemical Biology and Drug Discovery, Department of Chemistry, and School of Dental Medicine, Department of Oral Biology and Pathology, Stony Brook University, Stony Brook, New York 11794-3400, and.,From the Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, University of Wuerzburg, D-97080 Wuerzburg, Germany, the Institute of Pharmacy and Food Chemistry, University of Wuerzburg, Am Hubland, D-97074 Wuerzburg, Germany.,From the Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, University of Wuerzburg, D-97080 Wuerzburg, Germany, caroline.kisker@virchow.uni-wuerzburg.de.,School of Dental Medicine, Department of Oral Biology and Pathology, Stony Brook University, Stony Brook, New York 11794-3400, and.,the Rocky Mountain Regional Center of Excellence and Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523-1682.,the Institute for Chemical Biology and Drug Discovery, Department of Chemistry, and peter.tonge@stonybrook.edu.,the Institute for Chemical Biology and Drug Discovery, Department of Chemistry, and.,From the Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, University of Wuerzburg, D-97080 Wuerzburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADH]
A, B
270Escherichia coli (strain B / BL21-DE3)Mutation(s): 0 
EC: 1.3.1.9
Find proteins for A0A140NA83 (Escherichia coli (strain B / BL21-DE3))
Go to UniProtKB:  A0A140NA83
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
VT4
Query on VT4

Download SDF File 
Download CCD File 
A, B
2-hexyl-1-methyl-5-(2-methylphenoxy)pyridin-4(1H)-one
C19 H25 N O2
UMFLEDWOPZCDDL-UHFFFAOYSA-N
 Ligand Interaction
NAI
Query on NAI

Download SDF File 
Download CCD File 
A, B
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
NADH
C21 H29 N7 O14 P2
BOPGDPNILDQYTO-NNYOXOHSSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
VT4Ki: 7 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.176 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 79.678α = 90.00
b = 79.678β = 90.00
c = 330.150γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
SCALAdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-04-16
    Type: Initial release
  • Version 1.1: 2014-04-30
    Type: Database references
  • Version 1.2: 2014-08-13
    Type: Database references