Fig. 3.

Structure–kinetic relationship. (Top and Middle) Active site of the crystal structure of human CDK8/CycC in complex with the SKR compounds; residues of the CDK8 specific pockets and kinase regions are indicated with different colors, compounds are shown as sticks with their carbons colored yellow. H bonds are shown for compound/CDK8 interaction (blue dotted lines), water molecules that bridge interactions as blue nonbound spheres. Secondary structural elements are labeled black. Positioning of the figures was chosen to allow best view depending on the compound’s binding mode. Residence time and affinity are indicated. CDK8/CycC apo form in the DMG-in conformation: within the CDK8/CycC DMG-in conformation, M174^CDK8 is in close contact with F176^CDK8 in the deep pocket beyond the CDK8 αC helix. Y32^CDK8 side chain and activation segment (185–196) are disordered. Detection of residence time is reconciled in the compounds’ binding mode by H bonding with the hinge region (5 and 11); compounds with a long residence time form contacts within the front pocket (2, 1). Compound 7: M174^CDK8 is rotated outside the deep pocket to enable compound binding. Activation segment (178–194) is disordered. Compound 5: activation segment (177–193) is disordered; compound 11: activation segment (177–193) is disordered; compound 2: nearest distance to hinge region 5.1 Å; Y32^CDK8 side chain and activation segment (176–195) are disordered; compound 1: activation segment residues 176–195 are disordered. (Bottom) Interactions of compounds in relation to their residence time; the sum of the hydrophobic contacts per atom is plotted on the y axis; compound structures at the respective CDK8 kinase site, K_d values [µM], and residence time [min] are indicated. H bonds are marked in red numbers in the respective regions where they appear. As compound 11 forms no hydrophobic contact with the hinge region but two H bonds, the red label is shaded turquoise. The hydrophobic contacts were calculated as described in the text and SI Text. Parts of the kinase are indicated by color. Residues belonging to the same color are listed next to the plot.