Table 4.
Summary of the adenosine SuMD simulations performed on the inactive conformation of the A2A AR. For each replicate, the SuMD simulation time required, the positive or negative outcome, and the binding mode sampled at the end are reported along with the RMSDmin (calculated using 2YDO as a reference).
| SuMD Time (ns) | Reached the Orthosteric Site | Adenosine BINDING Mode | X-ray Binding Mode after 100 ns of MD | RMSDmin (Å) | |
|---|---|---|---|---|---|
| Replica 1i |
9.0 | No | No (Meta-binding site on ECL2) | - | 16.1 |
| Replica 2i |
16.8 | No | No (Meta-binding site on ECL2) | - | 13.6 |
| Replica 3i |
16.2 | Yes | No (Receptor Vestibule) | No (Receptor Vestibule) | 5.5 |
| Replica 4i |
31.2 | Yes | No (Receptor Vestibule) | No (Adenosine unbinding) | 6.1 |
| Replica 5i |
37.8 | Yes | No (Receptor Vestibule) | No (Receptor Vestibule) | 6.6 |
| Replica 6i |
24.6 | No | No (Meta-binding site on ECL2 | - | 15.4 |
| Replica 7i |
7.8 | No | No (Meta-binding site on ECL2) | - | 14.7 |
| Replica 8i |
7.8 | No | No (Meta-binding site on ECL2) | - | 13.8 |
| Replica 9i |
8.4 | Yes | No (Receptor Vestibule) | No (Adenosine unbinding) | 7.9 |
| Replica 10i |
45.6 | Yes | No (Receptor Vestibule) | Yes | 0.3 |