Cyclin-dependent kinases (CDKs) are activated upon cyclin-binding
to enable progression through the cell cycle. Dominant CDKs and cyclins
in mammalian cells include CDK1, CDK2, CDK4, and CDK6 and corresponding
cyclins A, B, D, and E. While only certain, “typical”
cyclin/CDK complexes are primarily responsible for cell cycle progression,
“atypical” cyclin/CDK complexes can form and sometimes
perform the same roles as typical complexes. We asked what structural
features of cyclins and CDKs favor the formation of typical complexes,
a vital yet not fully explored question. We use computational docking
and biophysical analyses to exhaustively evaluate the structure and
stability of all CDK and cyclin complexes listed above. We find that
binding of the complexes is generally stronger for typical than for
atypical complexes, especially when the CDK is in an active conformation.
Typical complexes have denser clusters, indicating that they have
more defined cyclin-binding sites than atypical complexes. Our results
help explain three notable features of cyclin/CDK function in the
cell cycle: (i) why CDK4 and cyclin-D have exceptionally high specificity
for each other; (ii) why both cyclin-A and cyclin-B strongly activate
CDK1, whereas CDK2 is only strongly activated by cyclin-A; and (iii)
why cyclin-E normally activates CDK2 but not CDK1. Overall, this work
reveals the binding modalities of cyclin/CDK complexes, how the modalities
lead to the preference for typical complexes versus atypical complexes,
and how binding modalities differ between typical complexes. Our observations
suggest targeting CDK catalytic actions through destabilizing their
native differential cyclin interfaces.