6ZGM

Crystal Structure of the VIM-2 Acquired Metallo-beta-Lactamase in Complex with the thiazolecarboxylate inhibitor ANT2681


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

ANT2681: SAR Studies Leading to the Identification of a Metallo-beta-lactamase Inhibitor with Potential for Clinical Use in Combination with Meropenem for the Treatment of Infections Caused by NDM-ProducingEnterobacteriaceae.

Davies, D.T.Leiris, S.Sprynski, N.Castandet, J.Lozano, C.Bousquet, J.Zalacain, M.Vasa, S.Dasari, P.K.Pattipati, R.Vempala, N.Gujjewar, S.Godi, S.Jallala, R.Sathyap, R.R.Darshanoju, N.A.Ravu, V.R.Juventhala, R.R.Pottabathini, N.Sharma, S.Pothukanuri, S.Holden, K.Warn, P.Marcoccia, F.Benvenuti, M.Pozzi, C.Mangani, S.Docquier, J.D.Lemonnier, M.Everett, M.

(2020) ACS Infect Dis 6: 2419-2430

  • DOI: https://doi.org/10.1021/acsinfecdis.0c00207
  • Primary Citation of Related Structures:  
    6ZGM

  • PubMed Abstract: 

    The clinical effectiveness of the important β-lactam class of antibiotics is under threat by the emergence of resistance, mostly due to the production of acquired serine- (SBL) and metallo-β-lactamase (MBL) enzymes. To address this resistance issue, multiple β-lactam/β-lactamase inhibitor combinations have been successfully introduced into the clinic over the past several decades. However, all of those combinations contain SBL inhibitors and, as yet, there are no MBL inhibitors in clinical use. Consequently, there exists an unaddressed yet growing healthcare problem due to the rise in recent years of highly resistant strains which produce New Delhi metallo (NDM)-type metallo-carbapenemases. Previously, we reported the characterization of an advanced MBL inhibitor lead compound, ANT431. Herein, we discuss the completion of a lead optimization campaign culminating in the discovery of the preclinical candidate ANT2681, a potent NDM inhibitor with strong potential for clinical development.


  • Organizational Affiliation

    Antabio SAS, 436 rue Pierre et Marie Curied, 31670 Labège, 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
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 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QKK (Subject of Investigation/LOI)
Query on QKK

Download Ideal Coordinates CCD File 
G [auth A]5-[[4-(carbamimidamidocarbamoylamino)-3,5-bis(fluoranyl)phenyl]sulfonylamino]-1,3-thiazole-4-carboxylic acid
C12 H11 F2 N7 O5 S2
MDBJDQPFGYPCRJ-UHFFFAOYSA-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: 1.65 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.96α = 90
b = 78.178β = 90
c = 79.659γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-02
    Type: Initial release
  • Version 1.1: 2020-09-23
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description