4BKU

Enoyl-ACP reductase FabI from Burkholderia pseudomallei with cofactor NADH and inhibitor PT155


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.137 
  • R-Value Observed: 0.138 

wwPDB Validation   3D Report Full Report


This is version 1.4 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:  
    4BKU, 4CUZ, 4CV0, 4CV1, 4CV2, 4CV3

  • 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 Staphylococcu ...

    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

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADH] A276Burkholderia pseudomallei 1026bMutation(s): 0 
Gene Names: fabIBP1026B_I1187
EC: 1.3.1.9
Find proteins for A0A0H3HP34 (Burkholderia pseudomallei (strain 1026b))
Explore A0A0H3HP34 
Go to UniProtKB:  A0A0H3HP34
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAI
Query on NAI

Download Ideal Coordinates CCD File 
A
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
C21 H29 N7 O14 P2
BOPGDPNILDQYTO-NNYOXOHSSA-N
 Ligand Interaction
1S5
Query on 1S5

Download Ideal Coordinates CCD File 
A
5-(4-amino-2-methylphenoxy)-2-hexyl-4-hydroxy-1-methylpyridinium
C19 H26 N2 O2
YALGUPBMXZEXMF-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.137 
  • R-Value Observed: 0.138 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.32α = 90
b = 75.95β = 90
c = 89.42γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-04-09
    Type: Initial release
  • Version 1.1: 2014-04-30
    Changes: Database references
  • Version 1.2: 2014-08-13
    Changes: Atomic model, Database references
  • Version 1.3: 2014-12-10
    Changes: Data collection
  • Version 1.4: 2017-06-28
    Changes: Data collection