Table 1.
Best binding site of palmitate in the ATP-binding cavity of the PKR, Akt1, CDK4 and MAPKAPK3 kinase domains. Best docking score (reflecting binding free-energy in kcal/mole) out of 10 ligand conformations are tabulated. Binding site for the docking experiments is defined as 5Å spheres around the side-chain heavy atoms for the tabulated residues in each case. According to the most negative docking scores, the most favorable binding site is near Lys296/Asp432 for PKR or analogous residues for the other kinases
| PKR | Akt1 | CDK4 | MAPKAPK3 | ||||
|---|---|---|---|---|---|---|---|
| K296 | −33.79 | K179 | −33.22 | K35 | −42.00 | K73 | Fail |
| D432 | −35.85 | D292 | −45.36 | D158 | Fail | D187 | −32.16 |
| I273 | −30.16 | L156 | Fail | I12 | −36.24 | L50 | −26.08 |
| V281 | Fail | V164 | Fail | V20 | Fail | V58 | Fail |
| F433 | Fail | F293 | Fail | F159 | Fail | F188 | Fail |
| V298 | Fail | L181 | Fail | V37 | Fail | L75 | Fail |
| F368 | −32.48 | Y229 | Fail | H95 | Fail | C120 | Fail |
| F421 | Fail | M281 | Fail | L147 | Fail | L173 | Fail |
| D414 | 414.68 | D274 | Fail | D140 | Fail | D166 | Fail |
| N419 | −26.60 | N279 | Fail | N145 | Fail | N171 | Fail |