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Table 1 Possible binding sites of NSP1 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    (7K3N) NSP1 of COVID-19
Amprenavir Known similar target molecule Protease, HIV-1
Binding properties 3 1 Superposition type R
RMSD 0.91 Å
Amino acid targets of drug 85GLY
86 ILE
58 PRO
No. of residues in known binding 24
Human similar targets 4
2 Superposition type L
RMSD 0.89 Å
Amino acid targets of drug 105 ILE
103 GLY
102 VAL
No. of residues in known binding 25
Human similar targets 4
3 Superposition type L
RMSD 0.94 Å
Amino acid targets of drug 24 ASP
83 LEU
97 VAL
No. of residues in known binding 28
Human similar targets 13
Atazanavir Known similar target molecule Protease, HIV-1
Binding properties 1 1 Superposition type R
RMSD 0.98 Å
Amino acid targets of drug 105 ILE
103 GLY
102 VAL
No. of residues in known binding 24
Human similar targets 5
Darunavir Known similar target molecule Pol polyprotein, HIV-2
Binding properties 10 1 Superposition type L
RMSD 0.91 Å
Amino acid targets of drug 105 ILE
103 GLY
102 VAL
No. of residues in known binding 27
Human similar targets 6
2 Superposition type L
RMSD 0.89 Å
Amino acid targets of drug 85 GLY
86 ILE
58 PRO
No. of residues in known binding 26
Human similar targets 0
3 Superposition type R
RMSD 1.47 Å
Amino acid targets of drug 98 LEU
29 VAL
99 VAL
No. of residues in known binding 20
Human similar targets 6
4 Superposition type L
RMSD 1.19 Å
Amino acid targets of drug 95 LEU
80 VAL
77 VAL
No. of residues in known binding 20
Human similar targets 6
5 Superposition type L
RMSD 1.40 Å
Amino acid targets of drug 79 LEU
26 VAL
60 VAL
No. of residues in known binding 20
Human similar targets 6
6 Superposition type L
RMSD 1.32 Å
Amino acid targets of drug 44 LEU
14 VAL
97 VAL
No. of residues in known binding 20
Human similar targets 6
7 Superposition type L
RMSD 1.16 Å
Amino acid targets of drug 83 LEU
60 VAL
26 VAL
No. of residues in known binding 20
Human similar targets 6
8 Superposition type L
RMSD 1.47 Å
Amino acid targets of drug 98 LEU
11 VAL
97 VAL
No. of residues in known binding 20
Human similar targets 6
9 Superposition type L
RMSD 1.11 Å
Amino acid targets of drug 55 LEU
60 VAL
99 VAL
No. of residues in known binding 20
Human similar targets 6
10 Superposition type L
RMSD 1.36 Å
Amino acid targets of drug 18 LEU
99 VAL
102 VAL
No. of residues in known binding 20
Human similar targets 6
Indinavir Known similar target molecule Protease retropepsin,
HIV-1
Binding properties 1 1 Superposition type R
RMSD 0.86 Å
Amino acid targets of drug 47 VAL
96 GLY
62 ILE
No. of residues in known binding 21
Human similar targets 3
Nelfinavir Known similar target molecule Protease,
HIV-1
Binding properties 2 1 Superposition type L
RMSD 1.16 Å
Amino acid targets of drug 110 ARG
95 LEU
75 VAL
No. of residues in known binding 30
Human similar targets 10
2 Superposition type L
RMSD 1.49 Å
Amino acid targets of drug 20 ARG
55 LEU
14 VAL
No. of residues in known binding 30
Human similar targets 10
Rimantadine Known similar target molecule M2 protein,
Influenza A/B
Binding properties 1 1 Superposition type R
RMSD 1.10 Å
Amino acid targets of drug 29 VAL
33 ALA
31 SER
No. of residues in known binding 10
Human similar targets 0
Saquinavir Known similar target molecule Protease, HIV-1
Binding properties 2 1 Superposition type R
RMSD 1.31 Å
Amino acid targets of drug 60 VAL
100 PRO
99 VAL
97 VAL
No. of residues in known binding 22
Human similar targets 6
2 Superposition type L
RMSD 0.92 Å
Amino acid targets of drug 105 ILE
103 GLY
102 VAL
No. of residues in known binding 31
Human similar targets 11
Tipranavir Known similar target molecule Protease, HIV-1
Binding properties 1 1 Superposition type L
RMSD 0.87 Å
Amino acid targets of drug 105 ILE
103 GLY
102 VAL
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, SER serine