Table 9.
Possible binding sites of NSP14 against known anti-viral drugs
| Drugs | Total binding sites | (5C8S) NSP14 of COVID-19 | |||
|---|---|---|---|---|---|
| Amprenavir | Known similar target molecule | Protease, HIV-1 | |||
| Binding properties | 3 | 1 | Superposition type | R | |
| RMSD | 0.83 Å | ||||
| Amino acid targets of drug |
88 GLY 87 ILE 412 PRO |
||||
| No. of residues in known binding | 24 | ||||
| Human similar targets | 4 | ||||
| 2 | Superposition type | L | |||
| RMSD | 0.72 Å | ||||
| Amino acid targets of drug |
170 LEU 162 VAL 166 ILE |
||||
| No. of residues in known binding | 18 | ||||
| Human similar targets | 4 | ||||
| 3 | Superposition type | L | |||
| RMSD | 0.87 Å | ||||
| Amino acid targets of drug |
31 ILE 17 GLY 14 ILE |
||||
| No. of residues in known binding | 24 | ||||
| Human similar targets | 6 | ||||
| Atazanavir | Known similar target molecule | Protease, HIV-1 | |||
| Binding properties | 1 | 1 | Superposition type | L | |
| RMSD | 0.66 Å | ||||
| Amino acid targets of drug |
78 ARG 107 PRO 108 VAL |
||||
| No. of residues in known binding | 23 | ||||
| Human similar targets | 3 | ||||
| Darunavir | Known similar target molecule | Protease, HIV-1 | |||
| Binding properties | 7 | 1 | Superposition type | L | |
| RMSD | 0.79 Å | ||||
| Amino acid targets of drug |
88 GLY 87 ILE 412 PRO |
||||
| No. of residues in known binding | 26 | ||||
| Human similar targets | 0 | ||||
| 2 | Superposition type | L | |||
| RMSD | 1.38 Å | ||||
| Amino acid targets of drug |
170 LEU 162 VAL 167 VAL 166 ILE |
||||
| No. of residues in known binding | 26 | ||||
| Human similar targets | 7 | ||||
| 3 | Superposition type | R | |||
| RMSD | 0.55 Å | ||||
| Amino acid targets of drug |
78 ARG 107 PRO 108 VAL |
||||
| No. of residues in known binding | 21 | ||||
| Human similar targets | 6 | ||||
| 4 | Superposition type | L | |||
| RMSD | 0.79 Å | ||||
| Amino acid targets of drug |
26 ALA 22 ASP 21 VAL |
||||
| No. of residues in known binding | 27 | ||||
| Human similar targets | 7 | ||||
| 5 | Superposition type | L | |||
| RMSD | 0.83 Å | ||||
| Amino acid targets of drug |
435 ALA 390 ASP 389 VAL |
||||
| No. of residues in known binding | 27 | ||||
| Human similar targets | 7 | ||||
| 6 | Superposition type | R | |||
| RMSD | 0.94 Å | ||||
| Amino acid targets of drug |
152 LEU 120 VAL 118 VAL |
||||
| No. of residues in known binding | 20 | ||||
| Human similar targets | 6 | ||||
| 7 | Superposition type | R | |||
| RMSD | 0.87 Å | ||||
| Amino acid targets of drug |
508 LEU 317 VAL 312 VAL |
||||
| No. of residues in known binding | 20 | ||||
| Human similar targets | 6 | ||||
| Grazoprevir | Known similar target molecule | NS3, NS4 Protease, Hepacivirus C | |||
| Binding properties | 1 | 1 | Superposition type | L | |
| RMSD | 0.90 Å | ||||
| Amino acid targets of drug |
65 GLN 52 GLY 127 GLY |
||||
| No. of residues in known binding | 17 | ||||
| Human similar targets | 7 | ||||
| Indinavir | Known similar target molecule | Polyprotein, HIV-1 | |||
| Binding properties | 1 | 1 | Superposition type | L | |
| RMSD | 0.82 Å | ||||
| Amino acid targets of drug |
78 ARG 107 PRO 108 VAL |
||||
| No. of residues in known binding | 24 | ||||
| Human similar targets | 1 | ||||
| Lopinavir | Known similar target molecule | Protease, HIV-1 | |||
| Binding properties | 2 | 1 | Superposition type | R | |
| RMSD | 0.65 Å | ||||
| Amino acid targets of drug |
78 ARG 107 PRO 108 VAL |
||||
| No. of residues in known binding | 27 | ||||
| Human similar targets | 6 | ||||
| 2 | Superposition type | R | |||
| RMSD | 0.94 Å | ||||
| Amino acid targets of drug |
31 ILE 17 GLY 14 ILE |
||||
| No. of residues in known binding | 27 | ||||
| Human similar targets | 4 | ||||
| Rimantadine | Known similar target molecule | M2 protein, Influeza A | |||
| Binding properties | 5 | 1 | Superposition type | L | |
| RMSD | 0.86 Å | ||||
| Amino acid targets of drug |
317 VAL 320 ALA 319 SER |
||||
| No. of residues in known binding | 10 | ||||
| Human similar targets | 0 | ||||
| 2 | Superposition type | L | |||
| RMSD | 0.90 Å | ||||
| Amino acid targets of drug |
32 ALA 33 SER 34 GLY |
||||
| No. of residues in known binding | 9 | ||||
| Human similar targets | 0 | ||||
| 3 | Superposition type | L | |||
| RMSD | 0.80 Å | ||||
| Amino acid targets of drug |
32 ALA 33 SER 35 GLY |
||||
| No. of residues in known binding | 9 | ||||
| Human similar targets | 0 | ||||
| 4 | Superposition type | R | |||
| RMSD | 0.67 Å | ||||
| Amino acid targets of drug |
01 ALA 0 SER -1 GLY |
||||
| No. of residues in known binding | 9 | ||||
| Human similar targets | 0 | ||||
| 5 | Superposition type | R | |||
| RMSD | 0.91 Å | ||||
| Amino acid targets of drug |
01 ALA 0 SER 102 GLY |
||||
| No. of residues in known binding | 9 | ||||
| Human similar targets | 0 | ||||
| Saquinavir | Known similar target molecule | Protease, HIV-1 | |||
| Binding properties | 2 | 1 | Superposition type | L | |
| RMSD | 0.90 Å | ||||
| Amino acid targets of drug |
31 ILE 17 GLY 14 ILE |
||||
| No. of residues in known binding | 21 | ||||
| Human similar targets | 4 | ||||
| 2 | Superposition type | R | |||
| RMSD | 0.90 Å | ||||
| Amino acid targets of drug |
84 ARG 244 VAL 277 THR |
||||
| No. of residues in known binding | 29 | ||||
| Human similar targets | 9 | ||||
| Tipranavir | Known similar target molecule | Protease, HIV-1 | |||
| Binding properties | 2 | 1 | Superposition type | L | |
| RMSD | 0.92 Å | ||||
| Amino acid targets of drug |
274 ALA 273 ASP 90 ASP |
||||
| No. of residues in known binding | 27 | ||||
| Human similar targets | 3 | ||||
| 2 | Superposition type | L | |||
| RMSD | 1.25 Å | ||||
| Amino acid targets of drug |
116 ASN 270 ALA 273 ASP 90 ASP |
||||
| No. of residues in known binding | 18 | ||||
| Human similar targets | 2 | ||||
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