5K9I

Crystal structure of c-SRC in complex with a covalent lysine probe

Summary for 5K9I

• Entry DOI: 10.2210/pdb5k9i/pdb
• Descriptor: Proto-oncogene tyrosine-protein kinase Src, 4-[(4-{4-[(3-cyclopropyl-1H-pyrazol-5-yl)amino]-6-[(prop-2-yn-1-yl)carbamoyl]pyrimidin-2-yl}piperazin-1-yl)methyl]benzene-1-sulfonyl fluoride (3 entities in total)
• Functional Keywords: covalent lysine probe, transferase
• Biological source: Gallus gallus (Chicken)
• Cellular location: Cell membrane : P00523
• Total number of polymer chains: 2
• Total formula weight: 66530.48

Authors

Wan, X.,Ouyang, S.,Zhao, Q.,Taunton, J. (deposition date: 2016-05-31, release date: 2017-02-01, Last modification date: 2024-10-16)

Primary citation

Zhao, Q.,Ouyang, X.,Wan, X.,Gajiwala, K.S.,Kath, J.C.,Jones, L.H.,Burlingame, A.L.,Taunton, J.
Broad-Spectrum Kinase Profiling in Live Cells with Lysine-Targeted Sulfonyl Fluoride Probes.
J. Am. Chem. Soc., 139:680-685, 2017

PubMed Abstract: Protein kinases comprise a large family of structurally related enzymes. A major goal in kinase-inhibitor development is to selectively engage the desired kinase while avoiding myriad off-target kinases. However, quantifying inhibitor interactions with multiple endogenous kinases in live cells remains an unmet challenge. Here, we report the design of sulfonyl fluoride probes that covalently label a broad swath of the intracellular kinome with high efficiency. Protein crystallography and mass spectrometry confirmed a chemoselective reaction between the sulfonyl fluoride and a conserved lysine in the ATP binding site. Optimized probe 2 (XO44) covalently modified up to 133 endogenous kinases, efficiently competing with high intracellular concentrations of ATP. We employed probe 2 and label-free mass spectrometry to quantify intracellular kinase engagement by the approved drug, dasatinib. The data revealed saturable dasatinib binding to a small subset of kinase targets at clinically relevant concentrations, highlighting the utility of lysine-targeted sulfonyl fluoride probes in demanding chemoproteomic applications.

PubMed: 28051857
DOI: 10.1021/jacs.6b08536

Experimental method

X-RAY DIFFRACTION (2.5 Å)