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Table 3 Possible binding sites of NSP5 against known anti-viral drugs.

From: Predicted antiviral drugs Darunavir, Amprenavir, Rimantadine and Saquinavir can potentially bind to neutralize SARS-CoV-2 conserved proteins

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
  1. 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