5L6P

EphB3 kinase domain covalently bound to an irreversible inhibitor (compound 6)

Summary for 5L6P

• Entry DOI: 10.2210/pdb5l6p/pdb
• Descriptor: Ephrin type-B receptor 3, ~{N}-(4-phenylazanylquinazolin-7-yl)ethanamide, 1,4-DIETHYLENE DIOXIDE, ... (4 entities in total)
• Functional Keywords: kinase, irreversible inhibitor, quinazoline, signaling, transferase
• Biological source: Homo sapiens (Human)
• Cellular location: Cell membrane ; Single-pass type I membrane protein : P54753
• Total number of polymer chains: 1
• Total formula weight: 34132.13

Authors

Schimpl, M.,Overman, R.,Kung, A.,Chen, Y.-C.,Ni, F.,Zhu, J.,Turner, M.,Molina, H.,Zhang, C. (deposition date: 2016-05-30, release date: 2016-08-10, Last modification date: 2024-10-09)

Primary citation

Kung, A.,Chen, Y.C.,Schimpl, M.,Ni, F.,Zhu, J.,Turner, M.,Molina, H.,Overman, R.,Zhang, C.
Development of Specific, Irreversible Inhibitors for a Receptor Tyrosine Kinase EphB3.
J.Am.Chem.Soc., 138:10554-10560, 2016

PubMed Abstract: Erythropoietin-producing human hepatocellular carcinoma (Eph) receptor tyrosine kinases (RTKs) regulate a variety of dynamic cellular events, including cell protrusion, migration, proliferation, and cell-fate determination. Small-molecule inhibitors of Eph kinases are valuable tools for dissecting the physiological and pathological roles of Eph. However, there is a lack of small-molecule inhibitors that are selective for individual Eph isoforms due to the high homology within the family. Herein, we report the development of the first potent and specific inhibitors of a single Eph isoform, EphB3. Through structural bioinformatic analysis, we identified a cysteine in the hinge region of the EphB3 kinase domain, a feature that is not shared with any other human kinases. We synthesized and characterized a series of electrophilic quinazolines to target this unique, reactive feature in EphB3. Some of the electrophilic quinazolines selectively and potently inhibited EphB3 both in vitro and in cells. Cocrystal structures of EphB3 in complex with two quinazolines confirmed the covalent linkage between the protein and the inhibitors. A "clickable" version of an optimized inhibitor was created and employed to verify specific target engagement in the whole proteome and to probe the extent and kinetics of target engagement of existing EphB3 inhibitors. Furthermore, we demonstrate that the autophosphorylation of EphB3 within the juxtamembrane region occurs in trans using a specific inhibitor. These exquisitely specific inhibitors will facilitate the dissection of EphB3's role in various biological processes and disease contribution.

PubMed: 27478969
DOI: 10.1021/jacs.6b05483

Experimental method

X-RAY DIFFRACTION (2.26 Å)