9LVH

Crystal structure of the mouse RIP3 kinase domain in complexed with Tricetin

Summary for 9LVH

• Entry DOI: 10.2210/pdb9lvh/pdb
• Descriptor: Receptor-interacting serine/threonine-protein kinase 3, 5,7-DIHYDROXY-2-(3,4,5-TRIHYDROXYPHENYL)-4H-CHROMEN-4-ONE (3 entities in total)
• Functional Keywords: mouse rip3 kinase domain, inhibitor, complex, transferase
• Biological source: Mus musculus (house mouse)
• Total number of polymer chains: 2
• Total formula weight: 73031.13

Authors

Xie, H.,Su, H.X.,Li, M.J.,Xu, Y.C. (deposition date: 2025-02-12, release date: 2025-05-07, Last modification date: 2025-05-21)

Primary citation

Xie, H.,Li, W.,Han, X.,Li, M.,Zhao, Q.,Xu, Y.,Su, H.,Meng, W.
Identification of RIPK3 as a target of flavonoids for anti-necroptosis in vitro.
Bioorg.Chem., 161:108503-108503, 2025

PubMed Abstract: Receptor-interacting protein kinase 3 (RIPK3), a key regulator of necroptosis, has emerged as an important target for therapeutic intervention. Flavonoids are natural compounds known for their anti-inflammatory and antioxidant properties, with recent studies highlighting their potential to modulate necroptosis. In this study, we explored the potential of RIPK3 as a target for flavonoids to achieve anti-necroptosis and anti-inflammatory effects. A library of 63 flavonoids was tested for RIPK3 binding and kinase inhibition using fluorescence polarization (FP) competition assay and ADP-Glo kinase activity assay. Six flavonoids, including scutellarein, robinetin, baicalin, myricetin, baicalein, and tricetin, showed significant inhibition of RIPK3, with IC values ranging from 2.5 to 13.7 μM. Structural studies of tricetin and robinetin through co-crystallization and molecular docking revealed distinct binding modes of these flavonoids within the ATP-binding pocket of RIPK3. The anti-necroptosis effects of these flavonoids were further evaluated in human HT-29 cells and mouse embryonic fibroblasts (MEFs) using a TSZ-induced cell death assay, resulting in EC values in the tens of micromolar range. Western blot analysis demonstrated that these flavonoids inhibit the phosphorylation of RIPK3 and its downstream effector, mixed lineage kinase domain-like protein (MLKL), and disrupt the formation of RIPK1 and RIPK3 aggregates in the necroptosis pathway. These findings identify RIPK3 as a target of natural flavonoids for the first time and elucidate the molecular mechanism underlying the anti-necroptotic activity of these flavonoids.

PubMed: 40328155
DOI: 10.1016/j.bioorg.2025.108503

Experimental method

X-RAY DIFFRACTION (2.38 Å)