6B22 | pdb_00006b22

Crystal structure OXA-24 beta-lactamase complexed with WCK 4234 by co-crystallization


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 
    0.198 (Depositor), 0.200 (DCC) 
  • R-Value Work: 
    0.177 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.178 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

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Literature

Strategic Approaches to Overcome Resistance against Gram-Negative Pathogens Using beta-Lactamase Inhibitors and beta-Lactam Enhancers: Activity of Three Novel Diazabicyclooctanes WCK 5153, Zidebactam (WCK 5107), and WCK 4234.

Papp-Wallace, K.M.Nguyen, N.Q.Jacobs, M.R.Bethel, C.R.Barnes, M.D.Kumar, V.Bajaksouzian, S.Rudin, S.D.Rather, P.N.Bhavsar, S.Ravikumar, T.Deshpande, P.K.Patil, V.Yeole, R.Bhagwat, S.S.Patel, M.V.van den Akker, F.Bonomo, R.A.

(2018) J Med Chem 61: 4067-4086

  • DOI: https://doi.org/10.1021/acs.jmedchem.8b00091
  • Primary Citation of Related Structures:  
    6B1F, 6B1H, 6B1J, 6B1W, 6B1X, 6B1Y, 6B22

  • PubMed Abstract: 

    Limited treatment options exist to combat infections caused by multidrug-resistant (MDR) Gram-negative bacteria possessing broad-spectrum β-lactamases. The design of novel β-lactamase inhibitors is of paramount importance. Here, three novel diazabicyclooctanes (DBOs), WCK 5153, zidebactam (WCK 5107), and WCK 4234 (compounds 1-3, respectively), were synthesized and biochemically characterized against clinically important bacteria. Compound 3 inhibited class A, C, and D β-lactamases with unprecedented k 2 / K values against OXA carbapenemases. Compounds 1 and 2 acylated class A and C β-lactamses rapidly but not the tested OXAs. Compounds 1-3 formed highly stable acyl-complexes as demonstrated by mass spectrometry. Crystallography revealed that 1-3 complexed with KPC-2 adopted a "chair conformation" with the sulfate occupying the carboxylate binding region. The cefepime-2 and meropenem-3 combinations were effective in murine peritonitis and neutropenic lung infection models caused by MDR Acinetobacter baumannii. Compounds 1-3 are novel β-lactamase inhibitors that demonstate potent cross-class inhibition, and clinical studies targeting MDR infections are warranted.


  • Organizational Affiliation

    Research Service , Louis Stokes Cleveland Department of Veterans Affairs Medical Center , 10701 East Boulevard , Cleveland , Ohio 44106 , United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-lactamase244Acinetobacter baumanniiMutation(s): 0 
Gene Names: blaOXA-33bla-OXA-40blaOXA-24blaOXA-40oxa-24oxa40
UniProt
Find proteins for Q8RLA6 (Acinetobacter baumannii)
Explore Q8RLA6 
Go to UniProtKB:  Q8RLA6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8RLA6
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free:  0.198 (Depositor), 0.200 (DCC) 
  • R-Value Work:  0.177 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.178 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.539α = 90
b = 102.539β = 90
c = 84.312γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted C8YClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
WockhardtUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-01
    Type: Initial release
  • Version 1.1: 2024-03-13
    Changes: Data collection, Database references