Pseudomonas aeruginosa LpxC in complex with a hydroxamate inhibitor

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.205 

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Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


Exploring the UDP pocket of LpxC through amino acid analogs.

Hale, M.R.Hill, P.Lahiri, S.Miller, M.D.Ross, P.Alm, R.Gao, N.Kutschke, A.Johnstone, M.Prince, B.Thresher, J.Yang, W.

(2013) Bioorg Med Chem Lett 23: 2362-2367

  • DOI: https://doi.org/10.1016/j.bmcl.2013.02.055
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Lipopolysaccharide (LPS) biosynthesis is an attractive antibacterial target as it is both conserved and essential for the survival of key pathogenic bacteria. Lipid A is the hydrophobic anchor for LPS and a key structural component of the outer membrane of Gram-negative bacteria. Lipid A biosynthesis is performed in part by a unique zinc dependent metalloamidase, LpxC (UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase), which catalyzes the first non-reversible step in lipid A biosynthesis. The UDP portion of the LpxC substrate-binding pocket has been relatively unexplored. We have designed and evaluated a series of hydroxamate based inhibitors which explore the SAR of substitutions directed into the UDP pocket with a range of substituted α-amino acid based linkers. We also provide the first wild type structure of Pseudomonas aeruginosa LpxC which was utilized in the design of many of these analogs.

  • Organizational Affiliation

    Infection Innovative Medicines Unit, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, MA 02451, USA. michael.hale@astrazeneca.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase
A, B
297Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: lpxCenvAPA4406
EC: 3.5.1
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP47205
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.205 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.762α = 90
b = 156.878β = 102.4
c = 49.334γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

  • Released Date: 2013-04-03 
  • Deposition Author(s): Lahiri, S.

Revision History  (Full details and data files)

  • Version 1.0: 2013-04-03
    Type: Initial release
  • Version 1.1: 2013-05-01
    Changes: Database references
  • Version 1.2: 2018-02-07
    Changes: Experimental preparation
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references, Derived calculations