8QKA

Structure of K. pneumoniae LpxH in complex with JEDI-852


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.221 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Antibiotic class with potent in vivo activity targeting lipopolysaccharide synthesis in Gram-negative bacteria.

Huseby, D.L.Cao, S.Zamaratski, E.Sooriyaarachchi, S.Ahmad, S.Bergfors, T.Krasnova, L.Pelss, J.Ikaunieks, M.Loza, E.Katkevics, M.Bobileva, O.Cirule, H.Gukalova, B.Grinberga, S.Backlund, M.Simoff, I.Leber, A.T.Berruga-Fernandez, T.Antonov, D.Konda, V.R.Lindstrom, S.Olanders, G.Brandt, P.Baranczewski, P.Vingsbo Lundberg, C.Liepinsh, E.Suna, E.Jones, T.A.Mowbray, S.L.Hughes, D.Karlen, A.

(2024) Proc Natl Acad Sci U S A 121: e2317274121-e2317274121

  • DOI: https://doi.org/10.1073/pnas.2317274121
  • Primary Citation of Related Structures:  
    8QJZ, 8QK2, 8QK5, 8QK9, 8QKA

  • PubMed Abstract: 

    Here, we describe the identification of an antibiotic class acting via LpxH, a clinically unexploited target in lipopolysaccharide synthesis. The lipopolysaccharide synthesis pathway is essential in most Gram-negative bacteria and there is no analogous pathway in humans. Based on a series of phenotypic screens, we identified a hit targeting this pathway that had activity on efflux-defective strains of Escherichia coli . We recognized common structural elements between this hit and a previously published inhibitor, also with activity against efflux-deficient bacteria. With the help of X-ray structures, this information was used to design inhibitors with activity on efflux-proficient, wild-type strains. Optimization of properties such as solubility, metabolic stability and serum protein binding resulted in compounds having potent in vivo efficacy against bloodstream infections caused by the critical Gram-negative pathogens E. coli and Klebsiella pneumoniae . Other favorable properties of the series include a lack of pre-existing resistance in clinical isolates, and no loss of activity against strains expressing extended-spectrum-β-lactamase, metallo-β-lactamase, or carbapenemase-resistance genes. Further development of this class of antibiotics could make an important contribution to the ongoing struggle against antibiotic resistance.


  • Organizational Affiliation

    Department of Medical Biochemistry and Microbiology, BMC, Uppsala University, Uppsala SE-75123, Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
UDP-2,3-diacylglucosamine hydrolase246Klebsiella pneumoniaeMutation(s): 0 
Gene Names: lpxH
EC: 3.6.1.54
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
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.221 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.013α = 90
b = 60.013β = 90
c = 284.658γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden--

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-17
    Type: Initial release