Table 1.
The calculated binding free energy and its components (kcal/mol) of PRMT5 with T1551 and EPZ015666 complexes based on the last 10, 20, and 40 ns MD trajectory.
| ΔEvdw | ΔEele | ΔGsol_np_GB | ΔGsol_polar_GB | ΔGGB | |
|---|---|---|---|---|---|
| PRMT5-T1551 | |||||
| Last 10 ns | –40.98 ± 0.13 | –29.73 ± 0.18 | –5.49 ± 0.01 | 44.08 ± 0.13 | –32.11 ± 0.14 |
| Last 20 ns | –41.69 ± 0.12 | –29.89 ± 0.16 | –5.57 ± 0.01 | 44.64 ± 0.12 | –32.50 ± 0.14 |
| Last 40 ns | –41.80 ± 0.12 | –30.89 ± 0.19 | –5.65 ± 0.01 | 45.32 ± 0.11 | –33.02 ± 0.15 |
| PRMT5-EPZ015666 | |||||
| Last 10 ns | –49.72 ± 0.15 | –43.09 ± 0.50 | –6.96 ± 0.01 | 59.67 ± 0.39 | –40.09 ± 0.18 |
| Last 20 ns | –48.98 ± 0.15 | –43.72 ± 0.48 | –6.94 ± 0.01 | 58.51 ± 0.38 | –41.13 ± 0.17 |
| Last 40 ns | –49.66 ± 0.17 | –49.51 ± 0.59 | –7.12 ± 0.01 | 64.17 ± 0.46 | –42.12 ± 0.19 |
ΔG was estimated from gas-phase energy and solvation free energy. The former contains an electrostatic term (ΔEele) and a van der Waals term (ΔEvdw). The latter is decomposed into polar (ΔGsol_polar) and non-polar solvation energy (ΔGsol_np).