Table 3.
Possible binding sites of NSP5 against known anti-viral drugs.
| Drugs | Total binding sites | (6M03) NSP5 of COVID-19 | |||
|---|---|---|---|---|---|
| Amphetamine | Known similar target molecule | Polymerase polyprotein, HIV-1 | |||
| Binding properties | 1 | 1 | Superposition type | L | |
| RMSD | 0.93 Å | ||||
| Amino acid targets of drug |
122 PRO 120 GLY 28 ASN |
||||
| No. of residues in known binding | 16 | ||||
| Human similar targets | 0 | ||||
| Darunavir | Known similar target molecule | HIV-1 protease | |||
| Binding properties | 2 | 1 | Superposition type | L | |
| RMSD | 1.06 Å | ||||
| Amino acid targets of drug |
109 GLY 200 ILE 293 PRO |
||||
| No. of residues in known binding | 26 | ||||
| Human similar targets | 0 | ||||
| 2 | Superposition type | R | |||
| RMSD | 0.76 Å | ||||
| Amino acid targets of drug |
133 ASN 195 GLY 194 ALA |
||||
| No. of residues in known binding | 26 | ||||
| Human similar targets | 2 | ||||
| Indinavir | Known similar target molecule |
Protease retropepsin, HIV-1 |
|||
| Binding properties | 1 | 1 | Superposition type | L | |
| RMSD | 0.81 Å | ||||
| Amino acid targets of drug |
106 ILE 109 GLY 200 ILE |
||||
| No. of residues in known binding | 22 | ||||
| Human similar targets | 4 | ||||
| Nelfinavir | Known similar target molecule |
Protease retropepsin, HIV-1 |
|||
| Binding properties | 1 | 1 | Superposition type | L | |
| RMSD | 1.05 Å | ||||
| Amino acid targets of drug |
153 ASP 292 THR 293 PRO |
||||
| No. of residues in known binding | 30 | ||||
| Human similar targets | 13 | ||||
| Nevirapine | Known similar target molecule |
Reverse transcriptase, HIV-1 |
|||
| Binding properties | 1 | 1 | Superposition type | R | |
| RMSD | 1.10 Å | ||||
| Amino acid targets of drug |
88 LYS 86 VAL 30 LEU |
||||
| No. of residues in known binding | 7 | ||||
| Human similar targets | 13 | ||||
| Ribavirin | Known similar target molecule |
RNA polymerase, Norwalk virus |
|||
| Binding properties | 1 | 1 | Superposition type | L | |
| RMSD | 1.06 Å | ||||
| Amino acid targets of drug |
198 THR 199 THR 238 ASN |
||||
| No. of residues in known binding | 9 | ||||
| Human similar targets | 2 | ||||
| Rimantadine | Known similar target molecule |
M2 protein, Influenza A |
|||
| Binding properties | 3 | 1 | Superposition type | R | |
| RMSD | 0.95 Å | ||||
| Amino acid targets of drug |
255 ALA 254 SER 251 GLY |
||||
| No. of residues in known binding | 9 | ||||
| Human similar targets | 0 | ||||
| 2 | Superposition type | L | |||
| RMSD | 0.88 Å | ||||
| Amino acid targets of drug |
255 ALA 254 SER 258 GLY |
||||
| No. of residues in known binding | 9 | ||||
| Human similar targets | 0 | ||||
| 3 | Superposition type | L | |||
| RMSD | 1.00 Å | ||||
| Amino acid targets of drug |
285 ALA 284 SER 283 GLY |
||||
| No. of residues in known binding | 9 | ||||
| Human similar targets | 0 | ||||
| Ritonavir | Known similar target molecule |
Polymerase polyprotein, HIV-1 |
|||
| Binding properties | 1 | 1 | Superposition type | L | |
| RMSD | 0.82 Å | ||||
| Amino acid targets of drug |
106 ILE 109 GLY 200 ILE |
||||
| No. of residues in known binding | 18 | ||||
| Human similar targets | 4 | ||||
| Tipranavir | Known similar target molecule |
Protease, HIV-1 |
|||
| Binding properties | 1 | 1 | Superposition type | L | |
| RMSD | 1.17 Å | ||||
| Amino acid targets of drug |
94 ALA 34 ASP 33 ASP |
||||
| 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, ASN asparagine, ALA alanine, THR threonine, LYS lysine, SER serine