This is a project exploring how various protein binding partners of human kinases (e.g. p27 for CDK4, p18 for CDK6) affect the binding of ATP, small-molecule kinase inhibitors (e.g. palbociclib), as well as proteolysis-targeting chimeras (PROTACs).
binding_pocket/
- analysis (i.e. structure superposition and docking) to quantify how CDK6 binding pocket changes shape and volume upon p18 binding.PROTAC_models
- construction and equilibration of structural models of kinase : PROTAC : E3 ligase adaptor ternary structures (with and without binding of p18/p27) in the following combination:- p18 : CDK6 : BSJ-03-123 : CRBN
- p27 : CDK4 : BSJ-03-123 : CRBN
- p18 : CDK6 : BSJ-05-017 : VHL
- p27 : CDK4 : BSJ-05-017 : VHL
- CDK6 : BSJ-03-123 : CRBN
- CDK4 : BSJ-03-123 : CRBN
- CDK6 : BSJ-05-017 : VHL
- CDK4 : BSJ-05-017 : VHL