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Table 7 Possible binding sites of NSP7-NSP8-NSP12 complex 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    (6M71) NSP7-NSP8-NSP12 complex of COVID-19
Amprenavir Known similar target molecule Protease, HIV-1
Binding properties 3 1 Superposition type L
RMSD 0.78 Å
Amino acid targets of drug 223 ILE
203 GLY
204 VAL
No. of residues in known binding 25
Human similar targets 4
2 Superposition type R
RMSD 0.66 Å
Amino acid targets of drug 201 ILE
203 GLY
204 VAL
No. of residues in known binding 25
Human similar targets 5
3 Superposition type L
RMSD 0.89 Å
Amino acid targets of drug 760 ASP
786 LEU
166 VAL
No. of residues in known binding 28
Human similar targets 11
  Known similar target molecule Protease, HIV-1
Atazanavir Binding properties 1 1 Superposition type R
RMSD 0.69 Å
Amino acid targets of drug 201 ILE
203 GLY
204 VAL
No. of residues in known binding 24
Human similar targets 4
Darunavir Known similar target molecule Protease, HIV-1
Binding properties 6 1 Superposition type L
RMSD 0.64 Å
Amino acid targets of drug 223 ILE
203 GLY
204 VAL
No. of residues in known binding 27
Human similar targets 6
2 Superposition type R
RMSD 0.69 Å
Amino acid targets of drug 201 ILE
203 GLY
204 VAL
No. of residues in known binding 27
Human similar targets 6
3 Superposition type R
RMSD 0.90 Å
Amino acid targets of drug 103 LEU
119 ILE
107 ILE
No. of residues in known binding 22
Human similar targets 12
4 Superposition type R
RMSD 0.74 Å
Amino acid targets of drug 102 ALA
106 ILE
53 VAL
No. of residues in known binding 19
Human similar targets 12
Indinavir Known similar target molecule Polyprotein, HIV-1
Binding properties 1 1 Superposition type L
RMSD 0.87 Å
Amino acid targets of drug 201 ILE
200 GLY
230 GLY
No. of residues in known binding 22
Human similar targets 7
Nelfinavir Known similar target molecule Protease, HIV-1
Binding properties 2 1 Superposition type L
RMSD 0.84 Å
Amino acid targets of drug 358 ASP
534 ASN
567 THR
No. of residues in known binding 30
Human similar targets 10
2 Superposition type R
RMSD 0.63 Å
Amino acid targets of drug 631 ARG
663 LEU
662 VAL
No. of residues in known binding 30
Human similar targets 10
Rimantadine Known similar target molecule M2 protein, Influeza A
Binding properties 1 1 Superposition type R
RMSD 0.91 Å
Amino acid targets of drug 771 ALA
772 SER
774 GLY
No. of residues in known binding 9
Human similar targets 0
Saquinavir Known similar target molecule Protease, HIV-1
Binding properties 3 1 Superposition type L
RMSD 0.73 Å
Amino acid targets of drug 820 VAL
830 PRO
817 THR
No. of residues in known binding 21
Human similar targets 6
2 Superposition type R
RMSD 0.91 Å
Amino acid targets of drug 623 ASP
678 GLY
462 THR
No. of residues in known binding 27
Human similar targets 0
3 Superposition type R
RMSD 0.61 Å
Amino acid targets of drug 201 ILE
203 GLY
204 VAL
No. of residues in known binding 31
Human similar targets 11
Tipranavir Known similar target molecule Protease, HIV-1
Binding properties 2 1 Superposition type L
RMSD 0.82 Å
Amino acid targets of drug 223 ILE
203 GLY
204 VAL
No. of residues in known binding 27
Human similar targets 3
2 Superposition type R
RMSD 0.58 Å
Amino acid targets of drug 201 ILE
203 GLY
204 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