9BLH

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

9BLH の概要

• エントリーDOI: 10.2210/pdb9blh/pdb
• 分子名称: 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)
• 機能のキーワード: kinase, protein kinase, phosphorylation, calcium/calmodulin, cytosolic, transferase-transferase inhibitor complex, ribociclib, transferase, transferase/transferase inhibitor
• 由来する生物種: Homo sapiens (human)
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 69233.78

構造登録者

Tomchick, D.R.,Majumdar, A.,Tagliabracci, V. (登録日: 2024-04-30, 公開日: 2025-05-07, 最終更新日: 2026-01-14)

主引用文献

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

実験手法

X-RAY DIFFRACTION (2.35 Å)