9LFV image
Deposition Date 2025-01-09
Release Date 2025-05-07
Last Version Date 2025-05-21
Entry Detail
PDB ID:
9LFV
Keywords:
Title:
Crystal structure of mouse RIP3 kinase domain complexed with LK01004
Biological Source:
Source Organism:
Mus musculus (Taxon ID: 10090)
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.78 Å
R-Value Free:
0.28
R-Value Work:
0.24
R-Value Observed:
0.24
Space Group:
P 1 21 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Receptor-interacting serine/threonine-protein kinase 3
Gene (Uniprot):Ripk3
Chain IDs:A, B, C, D
Chain Length:325
Number of Molecules:4
Biological Source:Mus musculus
Primary Citation
Structure-based design of potent and selective inhibitors targeting RIPK3 for eliminating on-target toxicity in vitro.
Nat Commun 16 4288 4288 (2025)
PMID: 40341069 DOI: 10.1038/s41467-025-59432-8

Abstact

The essential role of RIPK3 in necroptosis makes its inhibition a promising therapeutic strategy. However, the development of RIPK3 inhibitors has been hampered by on-target apoptosis and limited kinase selectivity. Inspired by the R69H mutation, which prevents on-target apoptosis by disrupting RIPK3 dimerization, we design LK-series inhibitors that effectively inhibit RIPK3 in biochemical assays and block TNF-α-induced necroptosis in both mouse L929 and human HT29 cells without inducing apoptosis. The representative compound, LK01003, shows high selectivity across a panel of 379 kinases. Our structural studies reveal that LK compounds act as Type I1/2 inhibitors, engaging a unique hydrophobic site and stabilizing an inactive conformation of RIPK3. Moreover, several type II inhibitors are also revealed to maintain RIPK3 in the inactive conformation and do not induce on-target apoptosis. These findings suggest a promising strategy for rational design of safe and selective inhibitors by locking the inactive conformation of RIPK3.

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Primary Citation of related structures