7LYE

Myotoxin I from Bothrops moojeni co-crystallized with synthetic inhibitor Varespladib (LY315920)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

The synthetic varespladib molecule is a multi-functional inhibitor for PLA 2 and PLA 2 -like ophidic toxins.

Salvador, G.H.M.Borges, R.J.Lomonte, B.Lewin, M.R.Fontes, M.R.M.

(2021) Biochim Biophys Acta Gen Subj 1865: 129913-129913

  • DOI: https://doi.org/10.1016/j.bbagen.2021.129913
  • Primary Citation of Related Structures:  
    7LYE

  • PubMed Abstract: 

    The treatment for snakebites is early administration of antivenom, which can be highly effective in inhibiting the systemic effects of snake venoms, but is less effective in the treatment of extra-circulatory and local effects. To complement standard-of-care treatments such as antibody-based antivenoms, natural and synthetic small molecules have been proposed for the inhibition of key venom components such as phospholipase A 2 (PLA 2 ) and PLA 2 -like toxins. Varespladib (compound LY315920) is a synthetic molecule developed and clinically tested aiming to block inflammatory cascades of several diseases associated with high PLA 2 s. Recent studies have demonstrated this molecule is able to potently inhibit snake venom catalytic PLA 2 and PLA 2 -like toxins. In vivo and in vitro techniques were used to evaluate the inhibitory effect of varespladib against MjTX-I. X-ray crystallography was used to reveal details of the interaction between these molecules. A new methodology that combines crystallography, mass spectroscopy and phylogenetic data was used to review its primary sequence. Varespladib was able to inhibit the myotoxic and cytotoxic effects of MjTX-I. Structural analysis revealed a particular inhibitory mechanism of MjTX-I when compared to other PLA 2 -like myotoxin, presenting an oligomeric-independent function. Results suggest the effectiveness of varespladib for the inhibition of MjTX-I, in similarity with other PLA 2 and PLA 2 -like toxins. Varespladib appears to be a promissory molecule in the treatment of local effects led by PLA 2 and PLA 2 -like toxins (oligomeric dependent and independent), indicating that this is a multifunctional or broadly specific inhibitor for different toxins within this superfamily.


  • Organizational Affiliation

    Departamento de Biofísica e Farmacologia, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu, SP, Brazil.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Basic phospholipase A2 homolog BomoTx
A, B, C, D
122Bothrops moojeniMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P82114 (Bothrops moojeni)
Explore P82114 
Go to UniProtKB:  P82114
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP82114
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.749α = 90
b = 128.595β = 106.6
c = 67.79γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-19
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Database references, Refinement description