7LYE

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

• PDB DOI: https://doi.org/10.2210/pdb7LYE/pdb

• Classification: TOXIN
• Organism(s): Bothrops moojeni
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2021-03-06 Released: 2021-05-19 
• Deposition Author(s): Salvador, G.H.M., Borges, R.J., Fontes, M.R.M.

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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 

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

• PubMed: 33865953 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: SAXS, light scattering

Macromolecule Content

• Total Structure Weight: 57.23 kDa 
• Atom Count: 4,330 
• Modelled Residue Count: 488 
• Deposited Residue Count: 488 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Basic phospholipase A2 homolog BomoTx	A, B, C, D	122	Bothrops moojeni	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P82114 (Bothrops moojeni) Explore P82114  Go to UniProtKB:  P82114

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
VRD (Subject of Investigation/LOI)	E [auth A], F [auth B], H [auth C], I [auth D]	({3-[amino(oxo)acetyl]-1-benzyl-2-ethyl-1H-indol-4-yl}oxy)acetic acid C21 H20 N2 O5 BHLXTPHDSZUFHR-UHFFFAOYSA-N
PE4	G [auth B]	2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL C16 H34 O8 PJWQOENWHPEPKI-UHFFFAOYSA-N

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 = 60.749	α = 90
b = 128.595	β = 106.6
c = 67.79	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-05-19 
Deposition Author(s): Salvador, G.H.M., Borges, R.J., Fontes, M.R.M.

Revision History  

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