Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 30.31 kDa 
• Atom Count: 2367 
• Residue Count: 257 
• Unique protein chains: 1

4BKU

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

• DOI: 10.2210/pdb4BKU/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Burkholderia pseudomallei 1026b
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-04-29 Released: 2014-04-09 
• Deposition Author(s): Hirschbeck, M.W., Liu, N., Neckles, C., Tonge, P.J., Kisker, C.

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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 

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

• PubMed: 24739388 
• 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 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.

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Organizational Affiliation: 

From the Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, University of Wuerzburg, D-97080 Wuerzburg, Germany, [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADH]	A	276	Burkholderia pseudomallei 1026b	Mutation(s): 0  Gene Names: fabI, BP1026B_I1187 EC: 1.3.1.9
Find proteins for A0A0H3HP34 (Burkholderia pseudomallei (strain 1026b)) Explore A0A0H3HP34  Go to UniProtKB:  A0A0H3HP34

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAI	A	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE C21 H29 N7 O14 P2 BOPGDPNILDQYTO-NNYOXOHSSA-N
1S5	A	5-(4-amino-2-methylphenoxy)-2-hexyl-4-hydroxy-1-methylpyridinium C19 H26 N2 O2 YALGUPBMXZEXMF-UHFFFAOYSA-O

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 = 74.32	α = 90
b = 75.95	β = 90
c = 89.42	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-04-29 
• Released Date: 2014-04-09 
Deposition Author(s): Hirschbeck, M.W., Liu, N., Neckles, C., Tonge, P.J., Kisker, C.

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