A Chemical Probe for Dark Kinase STK17B Derives Its Potency and High Selectivity through a Unique P‑Loop Conformation

STK17B is a member of the death-associated
protein kinase family
and has been genetically linked to the development of diverse diseases.
However, the role of STK17B in normal and disease pathology is poorly
defined. Here, we present the discovery of thieno­[3,2-d] pyrimidine SGC-STK17B-1 (11s), a high-quality chemical probe
for this understudied “dark” kinase. 11s is an ATP-competitive inhibitor that showed remarkable selectivity
over other kinases including the closely related STK17A. X-ray crystallography
of 11s and related thieno­[3,2-d]­pyrimidines bound to
STK17B revealed a unique P-loop conformation characterized by a salt
bridge between R41 and the carboxylic acid of the inhibitor. Molecular
dynamic simulations of STK17B revealed the flexibility of the P-loop
and a wide range of R41 conformations available to the apo-protein.
The isomeric thieno­[2,3-d]­pyrimidine SGC-STK17B-1N (19g) was identified as a negative control compound. The >100-fold
lower activity of 19g on STK17B was attributed to the
reduced basicity of its pyrimidine N1.