4LCH

Crystal structure of the Pseudomonas aeruginosa LPXC/LPC-051 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Synthesis, Structure, and Antibiotic Activity of Aryl-Substituted LpxC Inhibitors.

Liang, X.Lee, C.J.Zhao, J.Toone, E.J.Zhou, P.

(2013) J Med Chem 56: 6954-6966

  • DOI: 10.1021/jm4007774
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The zinc-dependent deacetylase LpxC catalyzes the committed step of lipid A biosynthesis in Gram-negative bacteria and is a validated target for the development of novel antibiotics to combat multidrug-resistant Gram-negative infections. Many potent ...

    The zinc-dependent deacetylase LpxC catalyzes the committed step of lipid A biosynthesis in Gram-negative bacteria and is a validated target for the development of novel antibiotics to combat multidrug-resistant Gram-negative infections. Many potent LpxC inhibitors contain an essential threonyl-hydroxamate headgroup for high-affinity interaction with LpxC. We report the synthesis, antibiotic activity, and structural and enzymatic characterization of novel LpxC inhibitors containing an additional aryl group in the threonyl-hydroxamate moiety, which expands the inhibitor-binding surface in LpxC. These compounds display enhanced potency against LpxC in enzymatic assays and superior antibiotic activity against Francisella novicida in cell culture. The comparison of the antibiotic activities of these compounds against a leaky Escherichia coli strain and the wild-type strain reveals the contribution of the formidable outer-membrane permeability barrier that reduces the compounds efficacy in cell culture and emphasizes the importance of maintaining a balanced hydrophobicity and hydrophilicity profile in developing effective LpxC-targeting antibiotics.


    Organizational Affiliation

    Structural Biology & Biophysics Program, Duke University, Durham, NC 27710, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylaseA299Pseudomonas aeruginosa PAO1Mutation(s): 1 
Gene Names: envAlpxCPA4406
EC: 3.5.1 (PDB Primary Data), 3.5.1.108 (UniProt)
Find proteins for P47205 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore P47205 
Go to UniProtKB:  P47205
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1WN
Query on 1WN

Download CCD File 
A
(betaS)-Nalpha-{4-[4-(4-aminophenyl)buta-1,3-diyn-1-yl]benzoyl}-N,beta-dihydroxy-beta-methyl-L-tyrosinamide
C27 H23 N3 O5
CXPNZJDYPDDMKA-SQHAQQRYSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
NO3
Query on NO3

Download CCD File 
A
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1WNKi :  0.024000000208616257   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.197α = 90
b = 73.527β = 90
c = 88.037γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
StructureStudiodata collection

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2013-06-21 
  • Released Date: 2013-08-21 
  • Deposition Author(s): Lee, C.-J., Zhou, P.

Revision History 

  • Version 1.0: 2013-08-21
    Type: Initial release
  • Version 1.1: 2013-09-25
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Advisory, Refinement description