7AYJ

Metallo beta-lactamse Vim-1 with a sulfamoyl inhibitor.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.21 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

Structural Basis of Metallo-beta-lactamase Inhibition by N -Sulfamoylpyrrole-2-carboxylates.

Farley, A.J.M.Ermolovich, Y.Calvopina, K.Rabe, P.Panduwawala, T.Brem, J.Bjorkling, F.Schofield, C.J.

(2021) ACS Infect Dis 7: 1809-1817

  • DOI: https://doi.org/10.1021/acsinfecdis.1c00104
  • Primary Citation of Related Structures:  
    7AYJ

  • PubMed Abstract: 

    Metallo-β-lactamases (MBLs) can efficiently catalyze the hydrolysis of all classes of β-lactam antibiotics except monobactams. While serine-β-lactamase (SBL) inhibitors (e.g., clavulanic acid, avibactam) are established for clinical use, no such MBL inhibitors are available. We report on the synthesis and mechanism of inhibition of N -sulfamoylpyrrole-2-carboxylates (NSPCs) which are potent inhibitors of clinically relevant B1 subclass MBLs, including NDM-1. Crystallography reveals that the N -sulfamoyl NH 2 group displaces the dizinc bridging hydroxide/water of the B1 MBLs. Comparison of crystal structures of an NSPC and taniborbactam (VRNX-5133), presently in Phase III clinical trials, shows similar binding modes for the NSPC and the cyclic boronate ring systems. The presence of an NSPC restores meropenem efficacy in clinically derived E. coli and K. pneumoniae bla NDM-1. The results support the potential of NSPCs and related compounds as efficient MBL inhibitors, though further optimization is required for their clinical development.


  • Organizational Affiliation

    Department of Chemistry, Chemistry Research Laboratory and the Ineos Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-lactamase VIM-1253Pseudomonas aeruginosaMutation(s): 0 
Gene Names: blaVIMblaVIM-1CAZ10_38240CAZ10_38245
EC: 3.5.2.6
UniProt
Find proteins for Q9XAY4 (Pseudomonas aeruginosa)
Explore Q9XAY4 
Go to UniProtKB:  Q9XAY4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9XAY4
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.21 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.533α = 90
b = 67.43β = 93.51
c = 40.267γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data scaling
PDB_EXTRACTdata extraction
PHASERphasing
DIALSdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom099141/Z/12/Z
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/S50676X/1
Medical Research Council (MRC, United Kingdom)United KingdomMR/N002679/1

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-12
    Type: Initial release
  • Version 1.1: 2021-05-26
    Changes: Database references
  • Version 1.2: 2021-06-02
    Changes: Database references
  • Version 1.3: 2021-06-23
    Changes: Database references
  • Version 1.4: 2024-01-31
    Changes: Data collection, Database references, Refinement description
  • Version 1.5: 2024-11-20
    Changes: Structure summary