Structural and binding studies of cyclin-dependent kinase 2 with NU6140 inhibitor.

Cyclin dependent kinase 2 (CDK2) is an established target protein for therapeutic intervention in various diseases, including cancer. Reported inhibitors of CDK2 target the ATP-binding pocket to inhibit the kinase activity. Many small molecule CDK2 inhibitors have been discovered and their crystal structure with CDK2 or CDK2/Cyclin A complex have been published. NU6140 is a CDK2 inhibitor with moderate potency and selectivity. Herein we report the co-crystal structure determination of NU6140 in complex with CDK2 and confirmation of the binding using various biophysical methods. Our data shows that NU6140 bind to CDK2 with a Kd of 800 nM as determined by SPR and stabilizes the protein against thermal denaturation (ΔTm- 5 ℃). The co-crystal structure determined in our study shows that NU6140 binds in the ATP binding pocket as expected for this class of compounds and interacts with Leu83 and Glu81 with regular hydrogen bonds and with Asp145 via water mediated H-bond. Based on these data, we propose structural modifications of NU6140 to introduce new interactions with CDK2 that can improve its potency while retaining the selectivity.