4FBX

Complex structure of human protein kinase CK2 catalytic subunit crystallized in the presence of a bisubstrate inhibitor

Summary for 4FBX

• Entry DOI: 10.2210/pdb4fbx/pdb
• Related: 1JWH 1LP4 3BQC 3NSZ 3OFM
• Related PRD ID: PRD_000870
• Descriptor: Casein kinase II subunit alpha, bisubstrate inhibitor, CHLORIDE ION, ... (4 entities in total)
• Functional Keywords: protein kinase fold, protein phosphorylation, bisubstrate inhibitor, transferase-transferase inhibitor complex, transferase/transferase inhibitor
• Biological source: Homo sapiens (human)
• Total number of polymer chains: 2
• Total formula weight: 41481.41

Authors

Enkvist, E.,Viht, K.,Bischoff, N.,Vahter, J.,Saaver, S.,Raidaru, G.,Issinger, O.-G.,Niefind, K.,Uri, A. (deposition date: 2012-05-23, release date: 2012-10-17, Last modification date: 2024-10-16)

Primary citation

Enkvist, E.,Viht, K.,Bischoff, N.,Vahter, J.,Saaver, S.,Raidaru, G.,Issinger, O.G.,Niefind, K.,Uri, A.
A subnanomolar fluorescent probe for protein kinase CK2 interaction studies.
Org.Biomol.Chem., 10:8645-8653, 2012

PubMed Abstract: Up-regulation of an acidophilic protein kinase, CK2, has been established in several types of cancer. This cognition has made CK2 an important target for drug development for cancer chemotherapy. The characterization of potential drug candidates, determination of the structure and clarification of the functions of CK2 could be facilitated by the application of small-molecule fluorescent probes that bind to the active site of the enzyme with high affinity and selectivity. We have used a bisubstrate approach for the development of a highly potent inhibitor of CK2. 4,5,6,7-Tetrabromo-1H-benzimidazole was conjugated with peptides containing multiple aspartate residues via different linkers. The design of the inhibitors was by crystallographic analysis of the complex of an inhibitor with the catalytic subunit of the enzyme (CK2α). The inhibitory potency of the synthesized compounds was established in a kinetic assay that used thin layer chromatography for the measurement of the rate of phosphorylation of fluorescently labelled peptide 5-TAMRA-RADDSDDDDD. The most potent inhibitor, ARC-1502 (K(i) = 0.5 nM), revealed high selectivity for CK2α in a panel of 140 protein kinases. Labelling of ARC-1502 with PromoFluor-647 gave the fluorescent probe ARC-1504 that possessed subnanomolar affinity towards both CK2α and the holoenzyme. The probe was used in a fluorescence anisotropy-based binding assay to measure the concentration of CK2α and characterize non-labelled ligands binding to the active site of CK2α.

PubMed: 23032938
DOI: 10.1039/c2ob26022k

Experimental method

X-RAY DIFFRACTION (2.33 Å)