5LCA

VIM-2 metallo-beta-lactamase in complex with 3-oxo-2-(3-(trifluoromethyl)phenyl)isoindoline-4-carboxylic acid (compound 17)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.130 
  • R-Value Observed: 0.134 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

NMR-filtered virtual screening leads to non-metal chelating metallo-beta-lactamase inhibitors.

Li, G.B.Abboud, M.I.Brem, J.Someya, H.Lohans, C.T.Yang, S.Y.Spencer, J.Wareham, D.W.McDonough, M.A.Schofield, C.J.

(2017) Chem Sci 8: 928-937

  • DOI: 10.1039/c6sc04524c
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • There are no clinically useful inhibitors of metallo-β-lactamases (MBLs), which are a growing problem because they hydrolyse almost all β-lactam antibacterials. Inhibition by most reported MBL inhibitors involves zinc ion chelation. A structure-based ...

    There are no clinically useful inhibitors of metallo-β-lactamases (MBLs), which are a growing problem because they hydrolyse almost all β-lactam antibacterials. Inhibition by most reported MBL inhibitors involves zinc ion chelation. A structure-based virtual screening approach combined with NMR filtering led to the identification of inhibitors of the clinically relevant Verona Integron-encoded MBL (VIM)-2. Crystallographic analyses reveal a new mode of MBL inhibition involving binding adjacent to the active site zinc ions, but which does not involve metal chelation. The results will aid efforts to develop new types of clinically useful inhibitors targeting MBLs/MBL-fold metallo-enzymes involved in antibacterial and anticancer drug resistance.


    Organizational Affiliation

    Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford , OX1 3TA , UK . Email: christopher.schofield@chem.ox.ac.uk ; Email: michael.mcdonough@chem.ox.ac.uk.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Metallo-beta-lactamase VIM-2A266Pseudomonas aeruginosaMutation(s): 0 
Gene Names: 
Find proteins for Q9K2N0 (Pseudomonas aeruginosa)
Explore Q9K2N0 
Go to UniProtKB:  Q9K2N0
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
B06
Query on B06

Download CCD File 
A
3-oxidanylidene-2-[3-(trifluoromethyl)phenyl]-1~{H}-isoindole-4-carboxylic acid
C16 H10 F3 N O3
UXSWDXQOTCKQJK-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
B06IC50:  32800   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.130 
  • R-Value Observed: 0.134 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.487α = 90
b = 65.313β = 90
c = 70.716γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
CrystalCleardata collection
HKL-3000data reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-02-15
    Type: Initial release
  • Version 1.1: 2017-05-24
    Changes: Database references