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 | ||||