Table 1.
Protein–ligand interaction profiler (PLIP) analysis for docking results of the ten clusters of SARS-CoV-2 RdRp
| SARS-CoV-2 RdRp conformation at | AutoDock Vina score (Kcal/mol) | H-bonding | Salt bridges | Hydrophobic interactions | |||
|---|---|---|---|---|---|---|---|
| Number | Residues involved in the interaction | Number | Residues involved in the interaction | Number | Residues involved in the interaction | ||
| 55.7 ns | − 7.6 | 7 | R555(2), Y619, D623(2), N691, and D760 | 3 | R624(3) | 1 | D623 |
| 93.3 ns | − 8.1 | 10 | Y619, K621, R624(2), D760, D761, W800, E811(2), and S814 | 2/1 | K551(2) and D760 | 2 | Y619 |
| 34.9 ns | − 7.5 | 7 | W617, D618, K621, D623, W800, E811, and S814 | 5 | K551(2), R555, K621, and R624 | 1 | D618 |
| 13.3 ns | − 6.9 | 5 | D760, D761(2), E811, and S814 | 2 | R836(2) | ||
| 28.1 ns | − 8.2 | 6 | S549, R555(2), R624(2), and N691 | 2 | R555 and R624 | 4 | Y455, K551, R553, and K621 |
| 40.1 ns | − 7.5 | 12 | K551, W617, D618, Y619, K621, C622, D623(2), D761(2), W800, and E811 | 1 | Y619 | ||
| 81.3 ns | − 8.0 | 8 | R555, Y619, D623(2), D760, D761(2), and W800 | 3 | K551, Y619, and D760 | ||
| 67.7 ns | − 6.7 | 5 | K621, D760, D761, E811, and S814 | 3 | R555(2), and R624 | 1 | Y619 |
| 19.7 ns | − 7.1 | 7 | D761(2), A797, E811, and S814(3) | 1 | E811 | 3 | K798, and E811 |
| 4.9 ns | − 7.0 | 7 | D618, D760, D761, W800, and S814(3) | 1 | R836 | ||
Italics residues are residues interacting through halogen bonds with sofosbuvir