8DND

Crystal structure of Bothrops pirajai Piratoxin-I (PrTX-I) and synthetic inhibitor Varespladib (LY315920)

  • Classification: TOXIN/ANTITOXIN
  • Organism(s): Bothrops pirajai
  • Mutation(s): No 

  • Deposited: 2022-07-11 Released: 2023-08-02 
  • Deposition Author(s): Salvador, G.H.M., Fontes, M.R.M.
  • Funding Organization(s): Sao Paulo Research Foundation (FAPESP), Brazilian National Council for Scientific and Technological Development (CNPq)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.193 

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This is version 1.1 of the entry. See complete history


Literature

Structural basis of the myotoxic inhibition of the Bothrops pirajai PrTX-I by the synthetic varespladib.

Salvador, G.H.M.Pinto, E.K.R.Ortolani, P.L.Fortes-Dias, C.L.Cavalcante, W.L.G.Soares, A.M.Lomonte, B.Lewin, M.R.Fontes, M.R.M.

(2023) Biochimie 207: 1-10

  • DOI: https://doi.org/10.1016/j.biochi.2022.11.006
  • Primary Citation of Related Structures:  
    8DND

  • PubMed Abstract: 

    Varespladib (LY315920) is a potent inhibitor of human group IIA phospholipase A 2 (PLA 2 ) originally developed to control inflammatory cascades of diseases associated with high or dysregulated levels of endogenous PLA 2 . Recently, varespladib was also found to inhibit snake venom PLA 2 and PLA 2 -like toxins. Herein, ex vivo neuromuscular blocking activity assays were used to test the inhibitory activity of varespladib. The binding affinity between varespladib and a PLA 2 -like toxin was quantified and compared with other potential inhibitors for this class of proteins. Crystallographic and bioinformatic studies showed that varespladib binds to PrTX-I and BthTX-I into their hydrophobic channels, similarly to other previously characterized PLA 2 -like myotoxins. However, a new finding is that an additional varespladib binds to the MDiS region, a particular site that is related to muscle cell disruption by these toxins. The present results further advance the characterization of the molecular interactions of varespladib with PLA 2 -like myotoxins and provide additional evidence for this compound as a promising inhibitor candidate for different PLA 2 and PLA 2 -like toxins.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Basic phospholipase A2 homolog piratoxin-1A [auth B],
B [auth A]
121Bothrops pirajaiMutation(s): 0 
UniProt
Find proteins for P58399 (Bothrops pirajai)
Explore P58399 
Go to UniProtKB:  P58399
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP58399
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.193 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.748α = 90
b = 72.66β = 90
c = 44.28γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Sao Paulo Research Foundation (FAPESP)Brazil2020/10143-7
Brazilian National Council for Scientific and Technological Development (CNPq)Brazil--

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-02
    Type: Initial release
  • Version 1.1: 2023-08-09
    Changes: Database references