2VAG

Crystal structure of di-phosphorylated human CLK1 in complex with a novel substituted indole inhibitor

Summary for 2VAG

• Entry DOI: 10.2210/pdb2vag/pdb
• Related: 1Z57
• Descriptor: DUAL SPECIFICITY PROTEIN KINASE CLK1, ethyl 3-[(E)-2-amino-1-cyanoethenyl]-6,7-dichloro-1-methyl-1H-indole-2-carboxylate (3 entities in total)
• Functional Keywords: serine/threonine-protein kinase, tyrosine-protein kinase, nucleus, transferase
• Biological source: HOMO SAPIENS (HUMAN)
• Cellular location: Nucleus: P49759
• Total number of polymer chains: 1
• Total formula weight: 40079.66

Authors

Pike, A.C.W.,Bullock, A.N.,Fedorov, O.,Pilka, E.S.,Ugochukwu, E.,von Delft, F.,Edwards, A.,Arrowsmith, C.H.,Weigelt, J.,Sundstrom, M.,Huber, K.,Bracher, F.,Knapp, S. (deposition date: 2007-08-31, release date: 2007-10-09, Last modification date: 2023-12-13)

Primary citation

Fedorov, O.,Huber, K.,Eisenreich, A.,Filippakopoulos, P.,King, O.,Bullock, A.N.,Szklarczyk, D.,Jensen, L.J.,Fabbro, D.,Trappe, J.,Rauch, U.,Bracher, F.,Knapp, S.
Specific Clk Inhibitors from a Novel Chemotype for Regulation of Alternative Splicing.
Chem.Biol, 18:67-, 2011

PubMed Abstract: There is a growing recognition of the importance of protein kinases in the control of alternative splicing. To define the underlying regulatory mechanisms, highly selective inhibitors are needed. Here, we report the discovery and characterization of the dichloroindolyl enaminonitrile KH-CB19, a potent and highly specific inhibitor of the CDC2-like kinase isoforms 1 and 4 (CLK1/CLK4). Cocrystal structures of KH-CB19 with CLK1 and CLK3 revealed a non-ATP mimetic binding mode, conformational changes in helix αC and the phosphate binding loop and halogen bonding to the kinase hinge region. KH-CB19 effectively suppressed phosphorylation of SR (serine/arginine) proteins in cells, consistent with its expected mechanism of action. Chemical inhibition of CLK1/CLK4 generated a unique pattern of splicing factor dephosphorylation and had at low nM concentration a profound effect on splicing of the two tissue factor isoforms flTF (full-length TF) and asHTF (alternatively spliced human TF).

PubMed: 21276940
DOI: 10.1016/J.CHEMBIOL.2010.11.009

Experimental method

X-RAY DIFFRACTION (1.8 Å)