8A4M

Crystal structure of the VIM-2 acquired metallo-beta-Lactamase in complex with compound 8 (JMV-7061)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Optimization of 1,2,4-Triazole-3-thiones toward Broad-Spectrum Metallo-beta-lactamase Inhibitors Showing Potent Synergistic Activity on VIM- and NDM-1-Producing Clinical Isolates.

Legru, A.Verdirosa, F.Vo-Hoang, Y.Tassone, G.Vascon, F.Thomas, C.A.Sannio, F.Corsica, G.Benvenuti, M.Feller, G.Coulon, R.Marcoccia, F.Devente, S.R.Bouajila, E.Piveteau, C.Leroux, F.Deprez-Poulain, R.Deprez, B.Licznar-Fajardo, P.Crowder, M.W.Cendron, L.Pozzi, C.Mangani, S.Docquier, J.D.Hernandez, J.F.Gavara, L.

(2022) J Med Chem 65: 16392-16419

  • DOI: https://doi.org/10.1021/acs.jmedchem.2c01257
  • Primary Citation of Related Structures:  
    8A4M, 8A76

  • PubMed Abstract: 

    Metallo-β-lactamases (MBLs) contribute to the resistance of Gram-negative bacteria to carbapenems, last-resort antibiotics at hospital, and MBL inhibitors are urgently needed to preserve these important antibacterial drugs. Here, we describe a series of 1,2,4-triazole-3-thione-based inhibitors displaying an α-amino acid substituent, which amine was mono- or disubstituted by (hetero)aryl groups. Compounds disubstituted by certain nitrogen-containing heterocycles showed submicromolar activities against VIM-type enzymes and strong NDM-1 inhibition ( K i = 10-30 nM). Equilibrium dialysis, native mass spectrometry, isothermal calorimetry (ITC), and X-ray crystallography showed that the compounds inhibited both VIM-2 and NDM-1 at least partially by stripping the catalytic zinc ions. These inhibitors also displayed a very potent synergistic activity with meropenem (16- to 1000-fold minimum inhibitory concentration (MIC) reduction) against VIM-type- and NDM-1-producing ultraresistant clinical isolates, including Enterobacterales and Pseudomonas aeruginosa . Furthermore, selected compounds exhibited no or moderate toxicity toward HeLa cells, favorable absorption, distribution, metabolism, excretion (ADME) properties, and no or modest inhibition of several mammalian metalloenzymes.


  • Organizational Affiliation

    IBMM, CNRS, Univ Montpellier, ENSCM, 34000 Montpellier, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Metallo-beta-lactamase VIM-2-like protein240Pseudomonas aeruginosaMutation(s): 0 
Gene Names: blaVIM
EC: 3.5.2.6
UniProt
Find proteins for B8QIQ9 (Pseudomonas aeruginosa)
Explore B8QIQ9 
Go to UniProtKB:  B8QIQ9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB8QIQ9
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
L2R (Subject of Investigation/LOI)
Query on L2R

Download Ideal Coordinates CCD File 
G [auth A](2~{S})-2-[bis(1~{H}-imidazol-4-ylmethyl)amino]-5-(3-phenyl-5-sulfanylidene-1~{H}-1,2,4-triazol-4-yl)pentanoic acid
C21 H24 N8 O2 S
YWCRDRKNQRFREX-SFHVURJKSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.883α = 90
b = 78.429β = 90
c = 80.036γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-26
    Type: Initial release
  • Version 1.1: 2024-02-07
    Changes: Data collection, Refinement description