K03861

K03861 is a type II inhibitor of CDK2. The cyclin-dependent kinase holoenzymes contain a catalytic subunit, the Cdk, a family of regulatory subunits, and the cyclins. Cdks are the catalytic subunits of the mammalian heterodimeric serine/threonine kinases progression, Cyclin-dependent kinases (CDKs) play important roles in the cell cycle regulation, transcription, and neuronal function. CDKs are frequently deregulated in some human tumours. The inhibitors targeted CDK are thought to prevent cell proliferation regulating cyclin-CDK complexes. The central role of CDKs in cell cycle regulation makes them a promising target for studying inhibitory molecules that can modify the cell proliferation [1].

K03861 is an aminopyrimidine-phenyl urea inhibitor of CDK2. The type II inhibitor CDK2 cocrystal structure of CDK2 with the inhibitor K03861 revealed a canonical type II binding mode. The type II inhibitors could compete with the binding of cyclins. The residues important for the type II inhibitors may be distant to the ATP binding pockets. The crystal structure of this complex may provide a foundation for the cyclin-competitive CDK2 inhibitors [2].

References:
Malumbres M, Barbacid M.  Mammalian cyclin-dependent kinases[J]. Trends in biochemical sciences, 2005, 30(11): 630-641.
Alexander L T, Mo?bitz H, Drueckes P, et al.  Type II inhibitors targeting CDK2[J]. ACS chemical biology, 2015, 10(9): 2116-2125.

Type II Inhibitors Targeting CDK2.[Pubmed:26158339]

ACS Chem Biol. 2015 Sep 18;10(9):2116-25.

Kinases can switch between active and inactive conformations of the ATP/Mg(2+) binding motif DFG, which has been explored for the development of type I or type II inhibitors. However, factors modulating DFG conformations remain poorly understood. We chose CDK2 as a model system to study the DFG in-out transition on a target that was thought to have an inaccessible DFG-out conformation. We used site-directed mutagenesis of key residues identified in structural comparisons in conjunction with biochemical and biophysical characterization of the generated mutants. As a result, we identified key residues that facilitate the DFG-out movement, facilitating binding of type II inhibitors. However, surprisingly, we also found that wild type CDK2 is able to bind type II inhibitors. Using protein crystallography structural analysis of the CDK2 complex with an aminopyrimidine-phenyl urea inhibitor (K03861) revealed a canonical type II binding mode and the first available type II inhibitor CDK2 cocrystal structure. We found that the identified type II inhibitors compete with binding of activating cyclins. In addition, analysis of the binding kinetics of the identified inhibitors revealed slow off-rates. The study highlights the importance of residues that may be distant to the ATP binding pocket in modulating the energetics of the DFG-out transition and hence inhibitor binding. The presented data also provide the foundation for a new class of slow off-rate cyclin-competitive CDK2 inhibitors targeting the inactive DFG-out state of this important kinase target.

AUZ 454 (K03861) is a type II CDK2 inhibitor with Kd of 8.2 nM. AUZ 454 (K03861) inhibits CDK2 activity by competing with binding of activating cyclins.

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