5A5Z

Approved Drugs Containing Thiols as Inhibitors of Metallo-beta- lactamases: Strategy To Combat Multidrug-Resistant Bacteria


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 5NBK


Literature

Approved Drugs Containing Thiols as Inhibitors of Metallo-beta-lactamases: Strategy To Combat Multidrug-Resistant Bacteria.

Klingler, F.M.Wichelhaus, T.A.Frank, D.Cuesta-Bernal, J.El-Delik, J.Muller, H.F.Sjuts, H.Gottig, S.Koenigs, A.Pos, K.M.Pogoryelov, D.Proschak, E.

(2015) J Med Chem 58: 3626-3630

  • DOI: https://doi.org/10.1021/jm501844d
  • Primary Citation of Related Structures:  
    5A5Z

  • PubMed Abstract: 

    Resistance to β-lactam antibiotics can be mediated by metallo-β-lactamase enzymes (MBLs). An MBL inhibitor could restore the effectiveness of β-lactams. We report on the evaluation of approved thiol-containing drugs as inhibitors of NDM-1, VIM-1, and IMP-7. Drugs were assessed by a novel assay using a purchasable fluorescent substrate and thermal shift. Best compounds were tested in antimicrobial susceptibility assay. Using these orthogonal screening methods, we identified drugs that restored the activity of imipenem.


  • Organizational Affiliation

    §Institute of Medical Microbiology and Infection Control, Paul-Ehrlich-Straße 40, 60596 Frankfurt, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
BETA-LACTAMASE NDM-1A,
B [auth C]
251Klebsiella pneumoniaeMutation(s): 0 
EC: 3.5.2.6
UniProt
Find proteins for C7C422 (Klebsiella pneumoniae)
Explore C7C422 
Go to UniProtKB:  C7C422
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC7C422
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.047α = 90
b = 108.047β = 90
c = 92.571γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-08
    Type: Initial release
  • Version 1.1: 2019-02-27
    Changes: Data collection, Database references, Experimental preparation, Other
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description