Table 1.
The simulation systems in this study.
| Systems | PDB entry | BD-unique binding residues | System size | Simulation time | Simulation Number | |
|---|---|---|---|---|---|---|
| ZA loop | BC loop | |||||
| BD1(BRD2)/RVX-208 | 2YDW + 4MR4 | Q101 | K157, D160, I162 | 30,716 atoms | 1 μs | 2 |
| BD1(BRD2) | 27,937 atoms | 1 μs | 1 | |||
| BD2(BRD2)/RVX-208 | 4MR6 | K374 | P430, H433, V435 | 29,291 atoms | 1 μs | 2 |
| BD2(BRD2) | 25,270 atoms | 1 μs | 1 | |||
| BD1(BRD4)/RVX-208 | 4MR4 | Q85 | K141, D144, I146 | 32,939 atoms | 1 μs | 2 |
| BD1(BRD4) | 30,088 atoms | 1 μs | 1 | |||
(Note: The residue number used in each system is corresponding to that in RCSB Protein Data Bank).