5U3B

Pseudomonas aeruginosa LpxC in complex with NVS-LPXC-01

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history. 


Literature

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 ...

    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.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
UDP-3-O-acyl-N-acetylglucosamine deacetylase
A, B
299Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: lpxC, envA, PA4406
EC: 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP47205
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
7TD
Query on 7TD
Download Ideal Coordinates CCD File 
D [auth A],
G [auth B]		N-[(2S)-3-amino-1-(hydroxyamino)-3-methyl-1-oxobutan-2-yl]-4-[(but-2-yn-1-yl)oxy]benzamide
C16 H21 N3 O4
JPCUWLVKAJJSLN-CYBMUJFWSA-N		 Ligand Interaction
EPE
Query on EPE
Download Ideal Coordinates CCD File 
E [auth A],
H [auth B]		4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
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

  • Method: X-RAY DIFFRACTION
  • 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
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data
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