6WII

Crystal structure of the K. pneumoniae LpxH/JH-LPH-41 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.162 

wwPDB Validation 3D Report Full Report



Literature

Synthesis and evaluation of sulfonyl piperazine LpxH inhibitors.

Kwak, S.H.Cochrane, C.S.Ennis, A.F.Lim, W.Y.Webster, C.G.Cho, J.Fenton, B.A.Zhou, P.Hong, J.

(2020) Bioorg Chem 102: 104055-104055

  • DOI: 10.1016/j.bioorg.2020.104055
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The UDP-2,3-diacylglucosamine pyrophosphate hydrolase LpxH is essential in lipid A biosynthesis and has emerged as a promising target for the development of novel antibiotics against multidrug-resistant Gram-negative pathogens. Recently, we reported ...

    The UDP-2,3-diacylglucosamine pyrophosphate hydrolase LpxH is essential in lipid A biosynthesis and has emerged as a promising target for the development of novel antibiotics against multidrug-resistant Gram-negative pathogens. Recently, we reported the crystal structure of Klebsiella pneumoniae LpxH in complex with 1 (AZ1), a sulfonyl piperazine LpxH inhibitor. The analysis of the LpxH-AZ1 co-crystal structure and ligand dynamics led to the design of 2 (JH-LPH-28) and 3 (JH-LPH-33) with enhanced LpxH inhibition. In order to harness our recent findings, we prepared and evaluated a series of sulfonyl piperazine analogs with modifications in the phenyl and N-acetyl groups of 3. Herein, we describe the synthesis and structure-activity relationship of sulfonyl piperazine LpxH inhibitors. We also report the structural analysis of an extended N-acyl chain analog 27b (JH-LPH-41) in complex with K. pneumoniae LpxH, revealing that 27b reaches an untapped polar pocket near the di-manganese cluster in the active site of K. pneumoniae LpxH. We expect that our findings will provide designing principles for new LpxH inhibitors and establish important frameworks for the future development of antibiotics against multidrug-resistant Gram-negative pathogens.


    Organizational Affiliation

    Department of Chemistry, Duke University, Durham, NC 27708, United States; Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, 27710, United States. Electronic address: jiyong.hong@duke.edu.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
UDP-2,3-diacylglucosamine hydrolaseA259Klebsiella pneumoniaeMutation(s): 0 
Gene Names: 
EC: 3.6.1.54
Find proteins for A0A1S0WIC1 (Klebsiella pneumoniae)
Explore A0A1S0WIC1 
Go to UniProtKB:  A0A1S0WIC1
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
U2V
Query on U2V

Download CCD File 
A
5-({[4-({4-[3-chloro-5-(trifluoromethyl)phenyl]piperazin-1-yl}sulfonyl)phenyl]carbamoyl}amino)-N-hydroxypentanamide
C23 H27 Cl F3 N5 O5 S
YNBLMVJKYWHKRJ-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
MN
Query on MN

Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.162 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.71α = 90
b = 105.71β = 90
c = 53.65γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI139216

Revision History 

  • Version 1.0: 2020-07-29
    Type: Initial release