4C1D

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.143 

Starting Model: experimental
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This is version 1.5 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: https://doi.org/10.1128/AAC.01335-15
  • Primary Citation of Related Structures:  
    4BZ3, 4C09, 4C1C, 4C1D, 4C1E, 4C1F, 4C1G, 4C1H

  • 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 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
BETA-LACTAMASE CLASS B VIM-2
A, B
242Pseudomonas aeruginosaMutation(s): 0 
EC: 3.5.2.6
UniProt
Find proteins for Q9K2N0 (Pseudomonas aeruginosa)
Explore Q9K2N0 
Go to UniProtKB:  Q9K2N0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9K2N0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
X8Z
Query on X8Z

Download Ideal Coordinates CCD File 
D [auth A],
K [auth B]
L-CAPTOPRIL
C9 H15 N O3 S
FAKRSMQSSFJEIM-RQJHMYQMSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
N [auth B]
O [auth B]
G [auth A],
H [auth A],
I [auth A],
N [auth B],
O [auth B],
P [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
FMT
Query on FMT

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
L [auth B],
M [auth B]
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
C [auth A],
J [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
X8Z BindingDB:  4C1D Ki: 630 (nM) from 1 assay(s)
IC50: min: 3500, max: 6600 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.143 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.246α = 90
b = 79.402β = 130.3
c = 67.774γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-08-27
    Type: Initial release
  • Version 1.1: 2014-09-17
    Changes: Other, Structure summary
  • Version 1.2: 2015-11-25
    Changes: Database references
  • Version 1.3: 2016-01-13
    Changes: Database references
  • Version 1.4: 2018-02-21
    Changes: Database references, Structure summary
  • Version 1.5: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description