Table 6.
An overview of key binding interactions and docking scores of the compounds with higher binding affinity towards SARS-CoV-2 main protease.
| Ligand number | PDB code | Hydrogen bonds | Other interactions | Docking score (kcal/mol) | ||
|---|---|---|---|---|---|---|
|
|
|
|||||
| Donor/acceptor | Bond length (Å) | Ligand | Cocrystallized ligand | |||
|
| ||||||
| 6 | 6W63 | Gln189/O | 2.28 | Asn142, Glu166, Leu141, His41 | −7.1 | −8.3 |
|
| ||||||
| 6XHM | NH/Glu166 | 1.92 | Met165, His41, Pro168, Ala191, r190 | −6.9 | −7.2 | |
| Glu166/O | 1.98 | |||||
| NH/Gln189 | 1.93 | |||||
| O/Gln189 | 2.91 | |||||
| His163/O | 2.30 | |||||
|
| ||||||
| 7D1M | His41/O | 2.14 | Met165, Asn142, Glu166 | −7.8 | −7.3 | |
| NH/Cys145 | 2.86 | |||||
| Cys145/O | 3.42 | |||||
| Ser144/O | 2.39 | |||||
| NH/Gln189 | 2.00 | |||||
|
| ||||||
| 8 | 6W63 | NH/Glu166 | 2.27 | Met165, Met49, His41, Pro168 | −6.9 | −8.3 |
| Gln189/O | 2.98 | |||||
| OH/Cys44 | 2.84 | |||||
|
| ||||||
| 6XHM | His41/O | 3.07 | Met49 | −6.6 | −7.2 | |
| Cys145/O | 3.65 | |||||
| Cys145/O | 2.39 | |||||
| His163/O | 1.99 | |||||
|
| ||||||
| 7D1M | His41/O | 2.67 | Met49 | −7.3 | −7.3 | |
| Cys145/O | 2.52 | |||||
| Ser144/O | 2.29 | |||||
| Ser144/O | 2.55 | |||||
| NH/Gln189 | 1.96 | |||||
| Gln189/O | 2.75 | |||||
| Glu166/O | 2.29 | |||||
|
| ||||||
| 17 | 6W63 | NH/Glu166 | 2.41 | Phe140, Asn142, Leu141, Met49, His41 | −8.1 | −8.3 |
| Gly143/O | 2.90 | |||||
| His163/N | 1.91 | |||||
| NH/Cys145 | 2.85 | |||||
|
| ||||||
| 6XHM | His163/N | 2.18 | Asn142, Leu141, Met165, His41, Met49 | −7.4 | −7.2 | |
| Cys145/O | 2.77 | |||||
| NH/His164 | 1.89 | |||||
| Gly143/O | 2.03 | |||||
|
| ||||||
| 7D1M | His41/O | 2.78 | Met49 | −7.8 | −7.3 | |
| His163/N | 2.49 | |||||
| NH/Cys145 | 3.71 | |||||
| Cys145/O | 3.72 | |||||
| NH/Asn142 | 2.44 | |||||
| NH/Gln189 | 2.29 | |||||