Pseudomonas aeruginosa LpxC in complex with NVS-LPXC-01

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 

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This is version 1.2 of the entry. See complete history


Design, Synthesis, and Properties of a Potent Inhibitor of Pseudomonas aeruginosa Deacetylase LpxC.

Piizzi, G.Parker, D.T.Peng, Y.Dobler, M.Patnaik, A.Wattanasin, S.Liu, E.Lenoir, F.Nunez, J.Kerrigan, J.McKenney, D.Osborne, C.Yu, D.Lanieri, L.Bojkovic, J.Dzink-Fox, J.Lilly, M.D.Sprague, E.R.Lu, Y.Wang, H.Ranjitkar, S.Xie, L.Wang, B.Glick, M.Hamann, L.G.Tommasi, R.Yang, X.Dean, C.R.

(2017) J Med Chem 60: 5002-5014

  • DOI: https://doi.org/10.1021/acs.jmedchem.7b00377
  • Primary Citation of Related Structures:  
    5U39, 5U3B

  • PubMed Abstract: 

    Over the past several decades, the frequency of antibacterial resistance in hospitals, including multidrug resistance (MDR) and its association with serious infectious diseases, has increased at alarming rates. Pseudomonas aeruginosa is a leading cause of nosocomial infections, and resistance to virtually all approved antibacterial agents is emerging in this pathogen. To address the need for new agents to treat MDR P. aeruginosa, we focused on inhibiting the first committed step in the biosynthesis of lipid A, the deacetylation of uridyldiphospho-3-O-(R-hydroxydecanoyl)-N-acetylglucosamine by the enzyme LpxC. We approached this through the design, synthesis, and biological evaluation of novel hydroxamic acid LpxC inhibitors, exemplified by 1, where cytotoxicity against mammalian cell lines was reduced, solubility and plasma-protein binding were improved while retaining potent anti-pseudomonal activity in vitro and in vivo.

  • Organizational Affiliation

    Infectious Diseases Area, Novartis Institutes for BioMedical Research , Emeryville, California 94608, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
UDP-3-O-acyl-N-acetylglucosamine deacetylase
A, B
299Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: lpxCenvAPA4406
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
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
7TD Binding MOAD:  5U3B IC50: 1.5 (nM) from 1 assay(s)
BindingDB:  5U3B IC50: 1.00e-3 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.826α = 90
b = 98.432β = 90
c = 165.187γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-06-07
    Type: Initial release
  • Version 1.1: 2017-07-05
    Changes: Database references
  • Version 1.2: 2024-03-06
    Changes: Data collection, Database references, Derived calculations