Table 3.
Binding interactions between the spike protein (PDB ID: 7DDN) and the ligands. The interactions are calculated using PLIP online server and Discovery Studio Visualizer for the docked complex.
| Ligand | Binding Energy (kcal/mol) | Hydrogen Bonds | VDW | Non-Covalent Interactions | Hydrophobic interactions |
|---|---|---|---|---|---|
| Ecamsule | -8.2 | Phe347 | Ala348 | Ala352 | Tyr351, Ala352, Asn450, Ile468, Thr470 |
| Eluxadoline | -8.0 | Tyr451, Ser349, Phe347, Ala352(2), Trp353 | Arg346, Asn450, Ile468 | Tyr351(π- πT shaped), Arg346, Ile468 | Ala352, Asn450, Ile468, Leu492 |
| Ergotamione | -8.0 | Ser349 Asn450(2) |
Ala352, Leu492 | Arg346 | Arg346, Ala348, Ala352, Leu452, Ile468, Thr470, Leu492 |
| Yaz | -8.0 | Tyr351 | NA | Ala348, Tyr351, Ala352, Ile468 | Ala348,352, Asn450, Ile468, Leu492 |
| Trosec | -7.2 | Ser349 | NA | Ala348,352 | Ala348,352, Asn450, Tyr451, Ile468, Leu492 |
| Naldemedine | -7.1 | Phe347, Ser349, Asn450 |
Asn450, Leu452,492 | Ala348,352 Leu452,492, Ile468 |
Leu452,492 Ile468, Phe490 |
| Conivaptan | -7.1 | Asn450 | Ala352, Ile468 | Ala,348,352(2), Arg346, Ile468 | Arg346, Ala348,352, Asn450, Ile468, Leu492 |
| Orap | -6.5 | Asn354 | Ala352 | Ala348, Ile468(halogen bond) |
Tyr351, Asn450, Leu452, Ile468 |
| Ponatinib | -6.5 | Ser349 | Ala348,352 | Ala348,352, (π-sigma) Tyr351(π-Tshaped) |
Ala348,352, Tyr351,451 Asn450, Thr470, Leu492 |