title: Structure and inhibitor specificity of the PCTAIRE-family kinase CDK16.
abstract: CDK16 (also known as PCTAIRE1 or PCTK1) is an atypical member of the cyclin-dependent kinase (CDK) family that has emerged as a key regulator of neurite outgrowth, vesicle trafficking and cancer cell proliferation. CDK16 is activated through binding to cyclin Y via a phosphorylation-dependent 14-3-3 interaction and has a unique consensus substrate phosphorylation motif compared with conventional CDKs. To elucidate the structure and inhibitor-binding properties of this atypical CDK, we screened the CDK16 kinase domain against different inhibitor libraries and determined the co-structures of identified hits. We discovered that the ATP-binding pocket of CDK16 can accommodate both type I and type II kinase inhibitors. The most potent CDK16 inhibitors revealed by cell-free and cell-based assays were the multitargeted cancer drugs dabrafenib and rebastinib. An inactive DFG-out binding conformation was confirmed by the first crystal structures of CDK16 in separate complexes with the inhibitors indirubin E804 and rebastinib, respectively. The structures revealed considerable conformational plasticity, suggesting that the isolated CDK16 kinase domain was relatively unstable in the absence of a cyclin partner. The unusual structural features and chemical scaffolds identified here hold promise for the development of more selective CDK16 inhibitors and provide opportunity to better characterise the role of CDK16 and its related CDK family members in various physiological and pathological contexts.
authors.affiliation: Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7DQ, U.K.
authors.forename: Sarah E
authors.initials: SE
authors.lastname: Dixon-Clarke
authors.affiliation: Nestlé Institute of Health Sciences SA, EPFL Innovation Park, bâtiment G, 1015 Lausanne, Switzerland.|School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
authors.forename: Saifeldin N
authors.initials: SN
authors.lastname: Shehata
authors.affiliation: Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7DQ, U.K.
authors.forename: Tobias
authors.initials: T
authors.lastname: Krojer
authors.affiliation: Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7DQ, U.K.
authors.forename: Timothy D
authors.initials: TD
authors.lastname: Sharpe
authors.affiliation: Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7DQ, U.K.|Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0QX, U.K.|Department of Biochemistry, University of Johannesburg, Auckland Park 2006, South Africa.
authors.forename: Frank
authors.initials: F
authors.lastname: von Delft
authors.affiliation: Nestlé Institute of Health Sciences SA, EPFL Innovation Park, bâtiment G, 1015 Lausanne, Switzerland.|School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
authors.forename: Kei
authors.initials: K
authors.lastname: Sakamoto
authors.affiliation: Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7DQ, U.K. alex.bullock@sgc.ox.ac.uk.
authors.forename: Alex N
authors.initials: AN
authors.lastname: Bullock
mesh_terms: D048948:14-3-3 Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D000255:Adenosine Triphosphate / Q000737:chemistry*; D000595:Amino Acid Sequence; D000970:Antineoplastic Agents / Q000737:chemistry*; D001665:Binding Sites; D003001:Cloning, Molecular; D018360:Crystallography, X-Ray; D018844:Cyclin-Dependent Kinases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D016213:Cyclins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D015870:Gene Expression; D006801:Humans; D007093:Imidazoles / Q000737:chemistry*; D007211:Indoles / Q000737:chemistry; D007700:Kinetics; D008024:Ligands; D010091:Oximes / Q000737:chemistry*; D010766:Phosphorylation; D011485:Protein Binding; D000072417:Protein Domains; D047428:Protein Kinase Inhibitors / Q000737:chemistry*; D017433:Protein Structure, Secondary; D011994:Recombinant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism
chemical_list: D048948:14-3-3 Proteins; D000970:Antineoplastic Agents; C543319:CCNY protein, human; D016213:Cyclins; D007093:Imidazoles; D007211:Indoles; D008024:Ligands; D010091:Oximes; D047428:Protein Kinase Inhibitors; D011994:Recombinant Proteins; D000255:Adenosine Triphosphate; D018844:Cyclin-Dependent Kinases; C089463:PCTAIRE-1 protein kinase; C561627:dabrafenib; C027185:indirubin
keywords: CCNY; PCTAIRE1; PCTK1; cyclin; kinase; phosphorylation