Table 5.
An overview of key binding interactions and docking scores of the compounds with lower 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 | |||
|
| ||||||
| 3 | 6W63 | OH/Asn142 | 2.37 | Met165, Asp187, Gln189, Cys44, Met49, His41 | −7.0 | −8.3 |
| NH/Glu166 | 2.94 | |||||
| Glu166/O | 2.90 | |||||
| Glu166/O | 1.97 | |||||
| His163/O | 2.91 | |||||
|
| ||||||
| 6XHM | Asn142/O | 2.29 | Met165, Gly143 | −6.8 | −7.2 | |
| His163/O | 2.23 | |||||
| NH/Cys145 | 2.75 | |||||
|
| ||||||
| 7D1M | His41/O | 2.84 | His163, Leu141, Ser144, Gln189, Glu166 | −7.0 | −7.1 | |
| Cys145/O | 3.38 | |||||
|
| ||||||
| 4 | 6W63 | OH/Asn142 | 3.38 | Glu166, Met165, Asp187, Gln189, Cys44, Met49, His41 | −7.0 | −7.4 |
|
| ||||||
| 6XHM | Glu166/O | 1.89 | Asn142, Leu141, His41, Met49, Pro168, Ala191, r190 | −6.9 | −7.2 | |
| NH/Gln189 | 2.43 | |||||
| Gln189/O | 2.76 | |||||
| NH/Cys145 | 2.88 | |||||
|
| ||||||
| 7D1M | His41/O | 2.55 | Met165, Leu141, His164, Ser144 | −7.2 | −7.0 | |
| NH/Gln189 | 2.05 | |||||
| Gln189/O | 2.53 | |||||
| Glu166/O | 2.43 | |||||
|
| ||||||
| 9 | 6W63 | NH/Glu166 | 2.55 | Asn142, His163, Met49, His41, Pro168 | −7.7 | −8.3 |
| Gln189/N | 2.65 | |||||
|
| ||||||
| 6XHM | His163/N | 2.56 | Asn142, Leu141, Cys145, Met165, His41, Gln189 | −7.7 | −7.2 | |
| NH/His164 | 1.86 | |||||
|
| ||||||
| 7D1M | His41/O | 2.37 | Met165, Leu141, Met49, Asn142, Gln189, Glu166 | −8.1 | −7.3 | |
| His163/N | 2.08 | |||||
| NH/His164 | 1.93 | |||||
|
| ||||||
| 10 | 6W63 | Glu166/O | 2.56 | Met165, Cys145, Gln189, Cys44, His41, Pro168 | −7.3 | −7.9 |
|
| ||||||
| 6XHM | Gly143/O | 2.72 | Asn142, Leu141, Cys145, Leu27, Met165, His41, Met49 | −7.3 | −7.2 | |
| Gln189/O | 2.69 | |||||
|
| ||||||
| 7D1M | Gln189/O | 2.17 | His41, Met165, Met49, Cys145, Asn142, Glu166 | −7.4 | −7.1 | |
|
| ||||||
| 11 | 6W63 | Glu166/O | 2.50 | Met165, Gln189, Met49, His41, Pro168 | −7.0 | −7.9 |
|
| ||||||
| 6XHM | NH/His164 | 2.83 | Asn142, Leu141, His41, Met49 | −7.2 | −7.2 | |
| Cys145/O | 3.32 | |||||
| Gly143/O | 2.75 | |||||
|
| ||||||
| 7D1M | NH/His164 | 2.80 | His41, Leu141, Met49, Asn142 | −7.3 | −7.3 | |
| Cys145/O | 3.50 | |||||
|
| ||||||
| 12 | 6W63 | Gln189/N | 2.45 | Glu166, Met165, Cys145, Met49, His41 | −7.3 | −8.3 |
|
| ||||||
| 6XHM | His163/F | 2.38 | Phe140, Leu141, Cys145 | −6.9 | −7.2 | |
| Gln189/O | 2.06 | |||||
|
| ||||||
| 7D1M | His172/F | 3.00 | Cys145, Asn142, Gln189, Glu166 | −7.7 | −7.3 | |
| NH/His164 | 2.65 | |||||
|
| ||||||
| 13 | 6W63 | Glu166/O | 2.43 | Met165, Cys145, Cys44, His41, Pro168 | −7.4 | −8.3 |
| Gln189/O | 2.34 | |||||
|
| ||||||
| 6XHM | Cys145/O | 3.79 | Asn142, Leu141, Glu166, Met165, His41, Met49, Gln189 | −6.6 | −7.0 | |
|
| ||||||
| 7D1M | Gln189/O | 2.10 | His41, Leu141, Met49, Cys145, Asn142 | −7.2 | −7.0 | |