8ZEM image
Deposition Date 2024-05-06
Release Date 2024-10-02
Last Version Date 2024-10-23
Entry Detail
PDB ID:
8ZEM
Keywords:
Title:
Crystal Structure of NLRP3 NACHT domain in complex with NP3-1
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Method Details:
Experimental Method:
Resolution:
3.32 Å
R-Value Free:
0.34
R-Value Work:
0.30
R-Value Observed:
0.30
Space Group:
P 61 2 2
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NACHT, LRR and PYD domains-containing protein 3
Gene (Uniprot):NLRP3
Chain IDs:A
Chain Length:551
Number of Molecules:1
Biological Source:Homo sapiens
Primary Citation
Deep-Learning-Driven Discovery of SN3-1, a Potent NLRP3 Inhibitor with Therapeutic Potential for Inflammatory Diseases.
J.Med.Chem. 67 17833 17854 (2024)
PMID: 39302813 DOI: 10.1021/acs.jmedchem.4c01857

Abstact

The NLRP3 inflammasome plays a central role in the pathogenesis of various intractable human diseases, making it an urgent target for therapeutic intervention. Here, we report the development of SN3-1, a novel orally potent NLRP3 inhibitor, designed through a lead compound strategy centered on deep-learning-based molecular generative models. Our strategy enables rapid fragment enumeration and takes into account the synthetic accessibility of the compounds, thereby significantly enhancing the optimization of lead compounds and facilitating the discovery of potent inhibitors. X-ray crystallography provided insights into the SN3-1 inhibitory mechanism. SN3-1 has shown a favorable safety profile in both acute and chronic toxicity assessments and exhibits robust pharmacokinetic properties. Furthermore, SN3-1 demonstrated significant therapeutic efficacy in various disease models characterized by NLRP3 activation. This study introduces a potent candidate for developing NLRP3 inhibitors and significantly expands the repertoire of tools available for the discovery of novel inhibitors.

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Primary Citation of related structures