4C1D

Crystal structure of the metallo-beta-lactamase VIM-2 with L-captopril


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.198 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.143 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structural Basis of Metallo-beta-Lactamase Inhibition by Captopril Stereoisomers.

Brem, J.van Berkel, S.S.Zollman, D.Lee, S.Y.Gileadi, O.McHugh, P.J.Walsh, T.R.McDonough, M.A.Schofield, C.J.

(2015) Antimicrob. Agents Chemother. 60: 142-150

  • DOI: 10.1128/AAC.01335-15
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • β-Lactams are the most successful antibacterials, but their effectiveness is threatened by resistance, most importantly by production of serine- and metallo-β-lactamases (MBLs). MBLs are of increasing concern because they catalyze the hydrolysis of a ...

    β-Lactams are the most successful antibacterials, but their effectiveness is threatened by resistance, most importantly by production of serine- and metallo-β-lactamases (MBLs). MBLs are of increasing concern because they catalyze the hydrolysis of almost all β-lactam antibiotics, including recent-generation carbapenems. Clinically useful serine-β-lactamase inhibitors have been developed, but such inhibitors are not available for MBLs. l-Captopril, which is used to treat hypertension via angiotensin-converting enzyme inhibition, has been reported to inhibit MBLs by chelating the active site zinc ions via its thiol(ate). We report systematic studies on B1 MBL inhibition by all four captopril stereoisomers. High-resolution crystal structures of three MBLs (IMP-1, BcII, and VIM-2) in complex with either the l- or d-captopril stereoisomer reveal correlations between the binding mode and inhibition potency. The results will be useful in the design of MBL inhibitors with the breadth of selectivity required for clinical application against carbapenem-resistant Enterobacteriaceae and other organisms causing MBL-mediated resistant infections.


    Organizational Affiliation

    Department of Chemistry, University of Oxford, Oxford, United Kingdom.,Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom.,Department of Chemistry, University of Oxford, Oxford, United Kingdom michael.mcdonough@chem.ox.ac.uk christopher.schofield@chem.ox.ac.uk.,Structural Genomics Consortium, University of Oxford, Oxford, United Kingdom.,Department of Microbiology and Infectious Diseases, Institute of Infection and Immunity, Heath Hospital, Cardiff, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BETA-LACTAMASE CLASS B VIM-2
A, B
242Pseudomonas aeruginosaMutation(s): 0 
Gene Names: bla vim-2 (bla-VIM-2, blasVIM-2, blaVIM-2, blaVIM2, VIM-2, vim-2)
Find proteins for Q9K2N0 (Pseudomonas aeruginosa)
Go to UniProtKB:  Q9K2N0
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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Download CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
X8Z
Query on X8Z

Download SDF File 
Download CCD File 
A, B
L-CAPTOPRIL
C9 H15 N O3 S
FAKRSMQSSFJEIM-RQJHMYQMSA-N
 Ligand Interaction
FMT
Query on FMT

Download SDF File 
Download CCD File 
A, B
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
X8ZIC50: 3500 nM (100) BINDINGDB
X8ZKd: 0 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.198 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.143 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 102.246α = 90.00
b = 79.402β = 130.30
c = 67.774γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
SCALEPACKdata scaling
DENZOdata reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-08-27
    Type: Initial release
  • Version 1.1: 2014-09-17
    Type: Other, Structure summary
  • Version 1.2: 2015-11-25
    Type: Database references
  • Version 1.3: 2016-01-13
    Type: Database references
  • Version 1.4: 2018-02-21
    Type: Database references, Structure summary