Table 2.
Possible binding sites of NSP3 against known anti-viral drugs
| Drugs | Total binding sites | (6WEY) NSP3 OF COVID-19 | |||
|---|---|---|---|---|---|
| Amprenavir | Known similar target molecule | Protease, HIV-1 | |||
| Binding properties | 4 | 1 | Superposition type | R | |
| RMSD | 1.13 Å | ||||
| Amino acid targets of drug |
335 ILE 252 GLY 253 VAL |
||||
| No. of residues in known binding | 25 | ||||
| Human similar targets | 2 | ||||
| 2 | Superposition type | R | |||
| RMSD | 1.21 Å | ||||
| Amino acid targets of drug |
335 ILE 337 GLY 304 VAL |
||||
| No. of residues in known binding | 25 | ||||
| Human similar targets | 2 | ||||
| 3 | Superposition type | R | |||
| RMSD | 1.01 Å | ||||
| Amino acid targets of drug |
270 ASP 287 LEU 300 VAL |
||||
| No. of residues in known binding | 28 | ||||
| Human similar targets | 11 | ||||
| 4 | Superposition type | R | |||
| RMSD | 0.88 Å | ||||
| Amino acid targets of drug |
214 LEU 359 VAL 222 ILE |
||||
| No. of residues in known binding | 18 | ||||
| Human similar targets | 5 | ||||
| Darunavir | Known similar target molecule | Protease, HIV-1 | |||
| Binding properties | 6 | 1 | Superposition type | R | |
| RMSD | 1.03 Å | ||||
| Amino acid targets of drug |
335 ILE 252 GLY 253 VAL |
||||
| No. of residues in known binding | 27 | ||||
| Human similar targets | 6 | ||||
| 2 | Superposition type | L | |||
| RMSD | 0.97 Å | ||||
| Amino acid targets of drug |
216 LEU 355 VAL 348 VAL |
||||
| No. of residues in known binding | 20 | ||||
| Human similar targets | 5 | ||||
| 3 | Superposition type | L | |||
| RMSD | 1.18 Å | ||||
| Amino acid targets of drug |
297 LEU 355 VAL 240 VAL |
||||
| No. of residues in known binding | 20 | ||||
| Human similar targets | 6 | ||||
| 4 | Superposition type | R | |||
| RMSD | 0.93 Å | ||||
| Amino acid targets of drug |
231 ALA 227 ILE 239 VAL |
||||
| No. of residues in known binding | 19 | ||||
| Human similar targets | 13 | ||||
| 5 | Superposition type | R | |||
| RMSD | 0.86 Å | ||||
| Amino acid targets of drug |
292 LEU 234 VAL 239 VAL |
||||
| No. of residues in known binding | 20 | ||||
| Human similar targets | 7 | ||||
| 6 | Superposition type | R | |||
| RMSD | 1.28 Å | ||||
| Amino acid targets of drug |
287 LEU 240 VAL 286 VAL |
||||
| No. of residues in known binding | 20 | ||||
| Human similar targets | 7 | ||||
| Rimantadine | Known similar target molecule | M2 protein, Influeza A | |||
| Binding properties | 2 | 1 | Superposition type | L | |
| RMSD | 0.94 Å | ||||
| Amino acid targets of drug |
333 ALA 332 SER 337 GLY |
||||
| No. of residues in known binding | 9 | ||||
| Human similar targets | 0 | ||||
| 2 | Superposition type | R | |||
| RMSD | 1.08 Å | ||||
| Amino acid targets of drug |
281 VAL 316 ALA 315 SER |
||||
| No. of residues in known binding | 9 | ||||
| Human similar targets | 0 | ||||
| Saquinavir | Known similar target molecule | Protease, HIV-1 | |||
| Binding properties | 1 | 1 | Superposition type | R | |
| RMSD | 1.25 Å | ||||
| Amino acid targets of drug |
335 ILE 252 GLY 253 VAL |
||||
| No. of residues in known binding | 31 | ||||
| Human similar targets | 12 | ||||
| Tipranavir | Known similar target molecule | Protease, HIV-1 | |||
| Binding properties | 2 | 1 | Superposition type | R | |
| RMSD | 1.14 Å | ||||
| Amino acid targets of drug |
335 ILE 337 GLY 304 VAL |
||||
| No. of residues in known binding | 27 | ||||
| Human similar targets | 3 | ||||
| 2 | Superposition type | R | |||
| RMSD | 1.10 Å | ||||
| Amino acid targets of drug |
335 ILE 252 GLY 253 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, SER serine