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Table 2 Possible binding sites of NSP3 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    (6WEY) NSP3 OF COVID-19
Amprenavir Known similar target molecule Protease, HIV-1
Binding properties 4 1 Superposition type R
RMSD 1.13 Å
Amino acid targets of drug 335 ILE
252 GLY
253 VAL
No. of residues in known binding 25
Human similar targets 2
2 Superposition type R
RMSD 1.21 Å
Amino acid targets of drug 335 ILE
337 GLY
304 VAL
No. of residues in known binding 25
Human similar targets 2
3 Superposition type R
RMSD 1.01 Å
Amino acid targets of drug 270 ASP
287 LEU
300 VAL
No. of residues in known binding 28
Human similar targets 11
4 Superposition type R
RMSD 0.88 Å
Amino acid targets of drug 214 LEU
359 VAL
222 ILE
No. of residues in known binding 18
Human similar targets 5
Darunavir Known similar target molecule Protease, HIV-1
Binding properties 6 1 Superposition type R
RMSD 1.03 Å
Amino acid targets of drug 335 ILE
252 GLY
253 VAL
No. of residues in known binding 27
Human similar targets 6
2 Superposition type L
RMSD 0.97 Å
Amino acid targets of drug 216 LEU
355 VAL
348 VAL
No. of residues in known binding 20
Human similar targets 5
3 Superposition type L
RMSD 1.18 Å
Amino acid targets of drug 297 LEU
355 VAL
240 VAL
No. of residues in known binding 20
Human similar targets 6
4 Superposition type R
RMSD 0.93 Å
Amino acid targets of drug 231 ALA
227 ILE
239 VAL
No. of residues in known binding 19
Human similar targets 13
5 Superposition type R
RMSD 0.86 Å
Amino acid targets of drug 292 LEU
234 VAL
239 VAL
No. of residues in known binding 20
Human similar targets 7
6 Superposition type R
RMSD 1.28 Å
Amino acid targets of drug 287 LEU
240 VAL
286 VAL
No. of residues in known binding 20
Human similar targets 7
Rimantadine Known similar target molecule M2 protein, Influeza A
Binding properties 2 1 Superposition type L
RMSD 0.94 Å
Amino acid targets of drug 333 ALA
332 SER
337 GLY
No. of residues in known binding 9
Human similar targets 0
2 Superposition type R
RMSD 1.08 Å
Amino acid targets of drug 281 VAL
316 ALA
315 SER
No. of residues in known binding 9
Human similar targets 0
Saquinavir Known similar target molecule Protease, HIV-1
Binding properties 1 1 Superposition type R
RMSD 1.25 Å
Amino acid targets of drug 335 ILE
252 GLY
253 VAL
No. of residues in known binding 31
Human similar targets 12
Tipranavir Known similar target molecule Protease, HIV-1
Binding properties 2 1 Superposition type R
RMSD 1.14 Å
Amino acid targets of drug 335 ILE
337 GLY
304 VAL
No. of residues in known binding 27
Human similar targets 3
2 Superposition type R
RMSD 1.10 Å
Amino acid targets of drug 335 ILE
252 GLY
253 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