5ACX

VIM-2-2, 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: 1.80 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.147 

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Ligand Structure Quality Assessment 


This is version 2.1 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: https://doi.org/10.1021/acs.jmedchem.5b01289
  • Primary Citation of Related Structures:  
    5ACU, 5ACV, 5ACW, 5ACX

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
BETA-LACTAMASE
A, B
266Pseudomonas 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
WL3
Query on WL3

Download Ideal Coordinates CCD File 
F [auth A],
M [auth B]
2-(4-fluorophenyl)carbonylbenzoic acid
C14 H9 F O3
FJAZVXUPZQSZKI-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
J [auth B]
K [auth B]
C [auth A],
D [auth A],
E [auth A],
J [auth B],
K [auth B],
L [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A],
O [auth B],
P [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
OH
Query on OH

Download Ideal Coordinates CCD File 
G [auth A],
N [auth B]
HYDROXIDE ION
H O
XLYOFNOQVPJJNP-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
OCS
Query on OCS
A, B
L-PEPTIDE LINKINGC3 H7 N O5 SCYS
Binding Affinity Annotations 
IDSourceBinding Affinity
WL3 Binding MOAD:  5ACX Kd: 9000 (nM) from 1 assay(s)
BindingDB:  5ACX Kd: 9000 (nM) from 1 assay(s)
IC50: 1.40e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.147 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.23α = 90
b = 79.22β = 130.18
c = 67.64γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata 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: 2015-11-04
    Type: Initial release
  • Version 1.1: 2015-11-25
    Changes: Database references
  • Version 1.2: 2018-06-27
    Changes: Advisory, Data collection, Derived calculations
  • Version 2.0: 2019-10-23
    Changes: Atomic model, Data collection, Other
  • Version 2.1: 2024-01-10
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description