9BLH

Crystal structure of calcium/calmodulin-dependent protein kinase type II subunit delta complexed with ribociclib

Summary for 9BLH

• Entry DOI: 10.2210/pdb9blh/pdb
• Descriptor: Calcium/calmodulin-dependent protein kinase type II subunit delta, 7-cyclopentyl-N,N-dimethyl-2-{[5-(piperazin-1-yl)pyridin-2-yl]amino}-7H-pyrrolo[2,3-d]pyrimidine-6-carboxamide (3 entities in total)
• Functional Keywords: kinase, protein kinase, phosphorylation, calcium/calmodulin, cytosolic, transferase-transferase inhibitor complex, ribociclib, transferase, transferase/transferase inhibitor
• Biological source: Homo sapiens (human)
• Total number of polymer chains: 2
• Total formula weight: 69233.78

Authors

Tomchick, D.R.,Majumdar, A.,Tagliabracci, V. (deposition date: 2024-04-30, release date: 2025-05-07, Last modification date: 2026-01-14)

Primary citation

Ye, J.S.,Majumdar, A.,Park, B.C.,Black, M.H.,Hsieh, T.S.,Osinski, A.,Servage, K.A.,Kulkarni, K.,Naidoo, J.,Alto, N.M.,Stratton, M.M.,Alfandari, D.,Ready, J.M.,Pawlowski, K.,Tomchick, D.R.,Tagliabracci, V.S.
Bacterial ubiquitin ligase engineered for small molecule and protein target identification.
Embo J., 2026

PubMed Abstract: The Legionella SidE effectors ubiquitinate host proteins independently of the canonical E1-E2 cascade. Here we engineer the SidE ligases to develop a modular proximity ligation approach for the identification of targets of small molecules and proteins, which we call SidBait. We validate the method with known small molecule-protein interactions and use it to identify CaMKII as an off-target interactor of the breast cancer drug ribociclib. Structural analysis and activity assays confirm that ribociclib binds the CaMKII active site and inhibits its activity. We further customize SidBait to identify protein-protein interactions and discover the F-actin capping protein (CapZ) as a target of the Legionella effector RavB during infection. Structural and biochemical studies indicate that RavB allosterically binds CapZ and decaps actin, thus functionally mimicking eukaryotic CapZ interacting proteins. Collectively, our results establish SidBait as a reliable tool for identifying targets of small molecules and proteins.

PubMed: 41484366
DOI: 10.1038/s44318-025-00665-0

Experimental method

X-RAY DIFFRACTION (2.35 Å)