7SS7

Crystal structure of Klebsiella LpxH in complex with JH-LPH-50


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.169 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Development of LpxH Inhibitors Chelating the Active Site Dimanganese Metal Cluster of LpxH.

Kwak, S.H.Skyler Cochrane, C.Cho, J.Dome, P.A.Ennis, A.F.Kim, J.H.Zhou, P.Hong, J.

(2023) ChemMedChem 18: e202300023-e202300023

  • DOI: https://doi.org/10.1002/cmdc.202300023
  • Primary Citation of Related Structures:  
    7SS6, 7SS7

  • PubMed Abstract: 

    Despite the widespread emergence of multidrug-resistant nosocomial Gram-negative bacterial infections and the major public health threat it brings, no new class of antibiotics for Gram-negative pathogens has been approved over the past five decades. Therefore, there is an urgent medical need for developing effective novel antibiotics against multidrug-resistant Gram-negative pathogens by targeting previously unexploited pathways in these bacteria. To fulfill this crucial need, we have been investigating a series of sulfonyl piperazine compounds targeting LpxH, a dimanganese-containing UDP-2,3-diacylglucosamine hydrolase in the lipid A biosynthetic pathway, as novel antibiotics against clinically important Gram-negative pathogens. Inspired by a detailed structural analysis of our previous LpxH inhibitors in complex with K. pneumoniae LpxH (KpLpxH), here we report the development and structural validation of the first-in-class sulfonyl piperazine LpxH inhibitors, JH-LPH-45 (8) and JH-LPH-50 (13), that achieve chelation of the active site dimanganese cluster of KpLpxH. The chelation of the dimanganese cluster significantly improves the potency of JH-LPH-45 (8) and JH-LPH-50 (13). We expect that further optimization of these proof-of-concept dimanganese-chelating LpxH inhibitors will ultimately lead to the development of more potent LpxH inhibitors for targeting multidrug-resistant Gram-negative pathogens.


  • Organizational Affiliation

    Department of Chemistry, Duke University, Durham, NC 27708, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
UDP-2,3-diacylglucosamine hydrolase259Klebsiella pneumoniaeMutation(s): 0 
Gene Names: lpxH_1lpxHC3483_19950NCTC9128_00880SAMEA104305404_03891
EC: 3.6.1.54
Membrane Entity: Yes 
UniProt
Find proteins for A6T5R0 (Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578))
Explore A6T5R0 
Go to UniProtKB:  A6T5R0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA6T5R0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BN8 (Subject of Investigation/LOI)
Query on BN8

Download Ideal Coordinates CCD File 
D [auth A]6-{[(4-{4-[3-chloro-5-(trifluoromethyl)phenyl]piperazine-1-sulfonyl}phenyl)carbamoyl]amino}-N-hydroxyhexanamide
C24 H29 Cl F3 N5 O5 S
GMLRUFCQNBOXDH-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
MN
Query on MN

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.169 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.53α = 90
b = 106.53β = 90
c = 53.56γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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  (Full details and data files)

  • Version 1.0: 2023-04-12
    Type: Initial release
  • Version 1.1: 2023-04-19
    Changes: Database references
  • Version 1.2: 2023-06-14
    Changes: Database references
  • Version 1.3: 2023-10-25
    Changes: Data collection, Refinement description