5ACV

VIM-2-OX, Discovery of novel inhibitor scaffolds against the metallo- beta-lactamase VIM-2 by SPR based fragment screening


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.963 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.162 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Discovery of Novel Inhibitor Scaffolds Against the Metallo-Beta-Lactamase Vim-2 by Spr Based Fragment Screening

Christopeit, T.Carlsen, T.J.O.Helland, R.Leiros, H.K.S.

(2015) J.Med.Chem. 58: 8671

  • DOI: 10.1021/acs.jmedchem.5b01289
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Metallo-β-lactamase (MBL) inhibitors can restore the function of carbapenem antibiotics and therefore help to treat infections of antibiotic resistant bacteria. In this study, we report novel fragments inhibiting the clinically relevant MBL Verona in ...

    Metallo-β-lactamase (MBL) inhibitors can restore the function of carbapenem antibiotics and therefore help to treat infections of antibiotic resistant bacteria. In this study, we report novel fragments inhibiting the clinically relevant MBL Verona integron-encoded metallo-β-lactamase (VIM-2). The fragments were identified from a library of 490 fragments using an orthogonal screening approach based on a surface plasmon resonance (SPR) based assay combined with an enzyme inhibition assay. The identified fragments showed IC50 values between 14 and 1500 μM and ligand efficiencies (LE) between 0.48 and 0.23 kcal/mol per heavy atom. For two of the identified fragments, crystal structures in complex with VIM-2 were obtained. The identified fragments represent novel inhibitor scaffolds and are good starting points for the design of potent MBL inhibitors. Furthermore, the established SPR based assay and the screening approach can be adapted to other MBLs and in this way improve the drug discovery process for this important class of drug targets.


    Organizational Affiliation

    Department of Chemistry, Faculty of Science and Technology, The Norwegian Structural Biology Centre (NorStruct), UiT The Arctic University of Norway , N-9037 Tromsø, Norway.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BETA-LACTAMASE
A, B
266Pseudomonas aeruginosaMutation(s): 0 
Gene Names: blaVIM-2 (bla vim-2, bla-VIM-2, blasVIM-2, blaVIM2, VIM-2, vim-2)
Find proteins for Q9K2N0 (Pseudomonas aeruginosa)
Go to UniProtKB:  Q9K2N0
Small Molecules
Ligands 3 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
CL
Query on CL

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
OH
Query on OH

Download SDF File 
Download CCD File 
A, B
HYDROXIDE ION
H O
XLYOFNOQVPJJNP-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
OCS
Query on OCS
A, B
L-PEPTIDE LINKINGC3 H7 N O5 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.963 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.162 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 100.709α = 90.00
b = 79.484β = 129.92
c = 66.845γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-11-04
    Type: Initial release
  • Version 1.1: 2015-11-25
    Type: Database references