8DND | pdb_00008dnd

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

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

(2023) Biochimie 207: 1-10

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.

Macromolecule Content

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Basic phospholipase A2 homolog piratoxin-1	A [auth B], B [auth A]	121	Bothrops pirajai	Mutation(s): 0
UniProt
Find proteins for P58399 (Bothrops pirajai) Explore P58399 Go to UniProtKB: P58399
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P58399
Sequence Annotations Expand
Reference Sequence

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
VRD (Subject of Investigation/LOI) Query on VRD Download:Ideal Coordinates CCD File SDF format, chain C [auth B] SDF format, chain D [auth B] SDF format, chain F [auth A] MOL2 format, chain C [auth B] MOL2 format, chain D [auth B] MOL2 format, chain F [auth A] mmCIF format, chain C [auth B] mmCIF format, chain D [auth B] mmCIF format, chain F [auth A]	C [auth B], D [auth B], F [auth A]	({3-[amino(oxo)acetyl]-1-benzyl-2-ethyl-1H-indol-4-yl}oxy)acetic acid C₂₁ H₂₀ N₂ O₅ BHLXTPHDSZUFHR-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Focus chain D [auth B] Focus chain F [auth A] Interactions & Density Focus chain C [auth B] Focus chain D [auth B] Focus chain F [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain E [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain E [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain E [auth B]	E [auth B], G [auth A], H [auth A], I [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth B] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain E [auth B] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A]