Table 10.
Possible binding sites of NSP15 against known anti-viral drugs
| Drugs | Total binding sites | (6VWW) NSP15 endoribonuclease of COVID-19 | |||
|---|---|---|---|---|---|
| Amprenavir | Known similar target molecule | Protease, HIV-1 | |||
| Binding properties | 2 | 1 | Superposition type | L | |
| RMSD | 0.90 Å | ||||
| Amino acid targets of drug |
72 ILE 157 GLY 156 VAL |
||||
| No. of residues in known binding | 25 | ||||
| Human similar targets | 4 | ||||
| 2 | Superposition type | L | |||
| RMSD | 0.66 Å | ||||
| Amino acid targets of drug |
251 LEU 276 VAL 296 ILE |
||||
| No. of residues in known binding | 19 | ||||
| Human similar targets | 5 | ||||
| Atazanavir | Known similar target molecule | Protease, HIV-1 | |||
| Binding properties | 1 | 1 | Superposition type | L | |
| RMSD | 0.83 Å | ||||
| Amino acid targets of drug |
72 ILE 157 GLY 156 VAL |
||||
| No. of residues in known binding | 24 | ||||
| Human similar targets | 4 | ||||
| Darunavir | Known similar target molecule | Protease, HIV-2 | |||
| Binding properties | 5 | 1 | Superposition type | L | |
| RMSD | 1.00 Å | ||||
| Amino acid targets of drug |
3 LEU 23 VAL 6 VAL |
||||
| No. of residues in known binding | 20 | ||||
| Human similar targets | 6 | ||||
| 2 | Superposition type | L | |||
| RMSD | 0.95 Å | ||||
| Amino acid targets of drug |
72 ILE 157 GLY 156 VAL |
||||
| No. of residues in known binding | 20 | ||||
| Human similar targets | 10 | ||||
| 3 | Superposition type | R | |||
| RMSD | 0.77 Å | ||||
| Amino acid targets of drug |
73 LEU 80 ILE 86 ILE |
||||
| No. of residues in known binding | 22 | ||||
| Human similar targets | 12 | ||||
| 4 | Superposition type | R | |||
| RMSD | 0.91 Å | ||||
| Amino acid targets of drug |
300 LEU 212 ILE 253 ILE |
||||
| No. of residues in known binding | 22 | ||||
| Human similar targets | 12 | ||||
| 5 | Superposition type | L | |||
| RMSD | 0.77 Å | ||||
| Amino acid targets of drug |
300 LEU 296 ILE 253 ILE |
||||
| No. of residues in known binding | 22 | ||||
| Human similar targets | 12 | ||||
| Indinavir | Known similar target molecule |
Protease retropepsin, HIV-1 |
|||
| Binding properties | 3 | 1 | Superposition type | R | |
| RMSD | 0.99 Å | ||||
| Amino acid targets of drug |
122 VAL 119 PRO 80 ILE |
||||
| No. of residues in known binding | 21 | ||||
| Human similar targets | 6 | ||||
| 2 | Superposition type | R | |||
| RMSD | 0.87 Å | ||||
| Amino acid targets of drug |
173 VAL 170 GLY 169 ILE |
||||
| No. of residues in known binding | 21 | ||||
| Human similar targets | 3 | ||||
| 3 | Superposition type | L | |||
| RMSD | 0.96 Å | ||||
| Amino acid targets of drug |
321 VAL 344 PRO 323 ILE |
||||
| No. of residues in known binding | 21 | ||||
| Human similar targets | 6 | ||||
| Lopinavir | Known similar target molecule |
Protease, HIV-1 |
|||
| Binding properties | 3 | 1 | Superposition type | R | |
| RMSD | 0.90 Å | ||||
| Amino acid targets of drug |
122 VAL 119 PRO 80 ILE |
||||
| No. of residues in known binding | 23 | ||||
| Human similar targets | 6 | ||||
| 2 | Superposition type | R | |||
| RMSD | 0.80 Å | ||||
| Amino acid targets of drug |
247 GLY 248 GLY 236 ILE |
||||
| No. of residues in known binding | 27 | ||||
| Human similar targets | 6 | ||||
| 3 | Superposition type | L | |||
| RMSD | 0.89 Å | ||||
| Amino acid targets of drug |
321 VAL 344 PRO 323 ILE |
||||
| No. of residues in known binding | 23 | ||||
| Human similar targets | 6 | ||||
| Saquinavir | Known similar target molecule | Protease, HIV-1 | |||
| Binding properties | 3 | 1 | Superposition type | L | |
| RMSD | 0.81 Å | ||||
| Amino acid targets of drug |
72 ILE 157 GLY 156 VAL |
||||
| No. of residues in known binding | 31 | ||||
| Human similar targets | 11 | ||||
| 2 | Superposition type | R | |||
| RMSD | 0.92 Å | ||||
| Amino acid targets of drug |
122 VAL 119 PRO 80 ILE |
||||
| No. of residues in known binding | 31 | ||||
| Human similar targets | 5 | ||||
| 3 | Superposition type | L | |||
| RMSD | 0.68 Å | ||||
| Amino acid targets of drug |
321 VAL 344 PRO 323 ILE |
||||
| No. of residues in known binding | 22 | ||||
| Human similar targets | 9 | ||||
| Tipranavir | Known similar target molecule | Protease, HIV-1 | |||
| Binding properties | 1 | 1 | Superposition type | L | |
| RMSD | 0.88 Å | ||||
| Amino acid targets of drug |
72 ILE 157 GLY 156 VAL |
||||
| No. of residues in known binding | 27 | ||||
| Human similar targets | 3 | ||||
| Torimifene | Known similar target molecule |
ENV, Glycoprotein-1, Zaire ebola virus |
|||
| Binding properties | 1 | 1 | Superposition type | L | |
| RMSD | 0.88 Å | ||||
| Amino acid targets of drug |
72 ILE 157 GLY 156 VAL |
||||
| No. of residues in known binding | 27 | ||||
| Human similar targets | 3 | ||||
Features of different drug binding motifs. HIV-1 Human Immunodeficiency virus 1, RMSD Root Mean Square Deviation, Å angstrom, ILE isoleucine, GLY glycine, VAL valine, LEU leucine, PRO proline, ASP aspartic acid