2. Details of Ternary Complex Structures .
| PROTAC | state | Cα-RMSD with 5T35 | Rg (Å) | PROTAC strain energy [kcal/mol] | ΔG bind [kcal/mol] | ΔG bind [kcal/mol] |
|---|---|---|---|---|---|---|
| MZ4 | global minimum state | 1.5 Å | 25.5 | 44.363 | –100.52 ± 5.23 | –24.33 ± 7.26 |
| specific state | 12.7 Å | 25.4 | 22.531 | –100.10 ± 5.61 | –22.14 ± 12.13 | |
| MZ1 | global minimum state | 2.0 Å | 25.5 | 40.291 | –104.44 ± 5.47 | –25.52 ± 6.56 |
| specific state | 12.8 Å | 27.4 | 16.712 | –97.64 ± 5.00 | –16.36 ± 4.95 | |
| MZ2 | global minimum state | 1.6 Å | 25.3 | 43.094 | –106.23 ± 5.53 | –24.76 ± 5.98 |
a
Cα-RMSD values were calculated based on the crystal structure with MZ1 (PDB ID: 5T35). The 100 structures around each minimum state were extracted to determine the binding free energy using MM/GBSA.