3PXR

Apo CDK2 crystallized from Jeffamine

Summary for 3PXR

• Entry DOI: 10.2210/pdb3pxr/pdb
• Related: 3PXF 3PXQ 3PXY 3PXZ 3PY0 3PY1
• Descriptor: Cell division protein kinase 2, 1,2-ETHANEDIOL (3 entities in total)
• Functional Keywords: protein kinase, cdk2, jeffamine, transferase
• Biological source: Homo sapiens (human)
• Total number of polymer chains: 1
• Total formula weight: 34823.42

Authors

Betzi, S.,Alam, R.,Schonbrunn, E. (deposition date: 2010-12-10, release date: 2011-02-16, Last modification date: 2023-09-13)

Primary citation

Betzi, S.,Alam, R.,Martin, M.,Lubbers, D.J.,Han, H.,Jakkaraj, S.R.,Georg, G.I.,Schonbrunn, E.
Discovery of a Potential Allosteric Ligand Binding Site in CDK2.
Acs Chem.Biol., 6:492-501, 2011

PubMed Abstract: Cyclin-dependent kinases (CDKs) are key regulatory enzymes in cell cycle progression and transcription. Aberrant activity of CDKs has been implicated in a number of medical conditions, and numerous small molecule CDK inhibitors have been reported as potential drug leads. However, these inhibitors exclusively bind to the ATP site, which is largely conserved among protein kinases, and clinical trials have not resulted in viable drug candidates, attributed in part to the lack of target selectivity. CDKs are unique among protein kinases, as their functionality strictly depends on association with their partner proteins, the cyclins. In an effort to identify potential target sites for disruption of the CDK-cyclin interaction, we probed the extrinsic fluorophore 8-anilino-1-naphthalene sulfonate (ANS) with human CDK2 and cyclin A using fluorescence spectroscopy and protein crystallography. ANS interacts with free CDK2 in a saturation-dependent manner with an apparent K(d) of 37 μM, and cyclin A displaced ANS from CDK2 with an EC(50) value of 0.6 μM. Co-crystal structures with ANS alone and in ternary complex with ATP site-directed inhibitors revealed two ANS molecules bound adjacent to one another, away from the ATP site, in a large pocket that extends from the DFG region above the C-helix. Binding of ANS is accompanied by substantial structural changes in CDK2, resulting in a C-helix conformation that is incompatible for cyclin A association. These findings indicate the potential of the ANS binding pocket as a new target site for allosteric inhibitors disrupting the interaction of CDKs and cyclins.

PubMed: 21291269
DOI: 10.1021/cb100410m

Experimental method

X-RAY DIFFRACTION (2 Å)