Figure 4.

CDK2 Pockets and Projections of Ensembles

(A) CDK2 in its holo conformation bound to two ANS molecules in the allosteric site (PDB: 3PXF). CDK2 is shown as a green cartoon with the two bound ANS shown as blue sticks. Pocket centers predicted by LIGSITE^cs are shown as purple spheres. The pockets are numbered by descending volume. Pocket 1 represents the ANS allosteric pocket. Pocket 2 represents the ATP binding pocket.

(B) Structures generated using ExProSE, with input structures the apo and holo structures (PDB: 1HCL and 3PXF, respectively), are shown as red dots. The axes are projections onto the first (x axis) and third (y axis) PCs of the ExProSE ensemble, which account for 35% and 8% of the motion, respectively. The blue dots represent the structures in the ensemble with perturbation at pocket centers 1–8 from (A).