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Table 9 Possible binding sites of NSP14 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

  

(5C8S) NSP14 of COVID-19

Amprenavir

Known similar target molecule

Protease, HIV-1

Binding properties

3

1

Superposition type

R

RMSD

0.83 Å

Amino acid targets of drug

88 GLY

87 ILE

412 PRO

No. of residues in known binding

24

Human similar targets

4

2

Superposition type

L

RMSD

0.72 Å

Amino acid targets of drug

170 LEU

162 VAL

166 ILE

No. of residues in known binding

18

Human similar targets

4

3

Superposition type

L

RMSD

0.87 Å

Amino acid targets of drug

31 ILE

17 GLY

14 ILE

No. of residues in known binding

24

Human similar targets

6

Atazanavir

Known similar target molecule

Protease, HIV-1

Binding properties

1

1

Superposition type

L

RMSD

0.66 Å

Amino acid targets of drug

78 ARG

107 PRO

108 VAL

No. of residues in known binding

23

Human similar targets

3

Darunavir

Known similar target molecule

Protease, HIV-1

Binding properties

7

1

Superposition type

L

RMSD

0.79 Å

Amino acid targets of drug

88 GLY

87 ILE

412 PRO

No. of residues in known binding

26

Human similar targets

0

2

Superposition type

L

RMSD

1.38 Å

Amino acid targets of drug

170 LEU

162 VAL

167 VAL

166 ILE

No. of residues in known binding

26

Human similar targets

7

3

Superposition type

R

RMSD

0.55 Å

Amino acid targets of drug

78 ARG

107 PRO

108 VAL

No. of residues in known binding

21

Human similar targets

6

4

Superposition type

L

RMSD

0.79 Å

Amino acid targets of drug

26 ALA

22 ASP

21 VAL

No. of residues in known binding

27

Human similar targets

7

5

Superposition type

L

RMSD

0.83 Å

Amino acid targets of drug

435 ALA

390 ASP

389 VAL

No. of residues in known binding

27

Human similar targets

7

6

Superposition type

R

RMSD

0.94 Å

Amino acid targets of drug

152 LEU

120 VAL

118 VAL

No. of residues in known binding

20

Human similar targets

6

7

Superposition type

R

RMSD

0.87 Å

Amino acid targets of drug

508 LEU

317 VAL

312 VAL

No. of residues in known binding

20

Human similar targets

6

Grazoprevir

Known similar target molecule

NS3, NS4 Protease, Hepacivirus C

Binding properties

1

1

Superposition type

L

RMSD

0.90 Å

Amino acid targets of drug

65 GLN

52 GLY

127 GLY

No. of residues in known binding

17

Human similar targets

7

Indinavir

Known similar target molecule

Polyprotein, HIV-1

Binding properties

1

1

Superposition type

L

RMSD

0.82 Å

Amino acid targets of drug

78 ARG

107 PRO

108 VAL

No. of residues in known binding

24

Human similar targets

1

Lopinavir

Known similar target molecule

Protease, HIV-1

Binding properties

2

1

Superposition type

R

RMSD

0.65 Å

Amino acid targets of drug

78 ARG

107 PRO

108 VAL

No. of residues in known binding

27

Human similar targets

6

2

Superposition type

R

RMSD

0.94 Å

Amino acid targets of drug

31 ILE

17 GLY

14 ILE

No. of residues in known binding

27

Human similar targets

4

Rimantadine

Known similar target molecule

M2 protein, Influeza A

Binding properties

5

1

Superposition type

L

RMSD

0.86 Å

Amino acid targets of drug

317 VAL

320 ALA

319 SER

No. of residues in known binding

10

Human similar targets

0

2

Superposition type

L

RMSD

0.90 Å

Amino acid targets of drug

32 ALA

33 SER

34 GLY

No. of residues in known binding

9

Human similar targets

0

3

Superposition type

L

RMSD

0.80 Å

Amino acid targets of drug

32 ALA

33 SER

35 GLY

No. of residues in known binding

9

Human similar targets

0

4

Superposition type

R

RMSD

0.67 Å

Amino acid targets of drug

01 ALA

0 SER

-1 GLY

No. of residues in known binding

9

Human similar targets

0

5

Superposition type

R

RMSD

0.91 Å

Amino acid targets of drug

01 ALA

0 SER

102 GLY

No. of residues in known binding

9

Human similar targets

0

Saquinavir

Known similar target molecule

Protease, HIV-1

Binding properties

2

1

Superposition type

L

RMSD

0.90 Å

Amino acid targets of drug

31 ILE

17 GLY

14 ILE

No. of residues in known binding

21

Human similar targets

4

2

Superposition type

R

RMSD

0.90 Å

Amino acid targets of drug

84 ARG

244 VAL

277 THR

No. of residues in known binding

29

Human similar targets

9

Tipranavir

Known similar target molecule

Protease, HIV-1

Binding properties

2

1

Superposition type

L

RMSD

0.92 Å

Amino acid targets of drug

274 ALA

273 ASP

90 ASP

No. of residues in known binding

27

Human similar targets

3

2

Superposition type

L

RMSD

1.25 Å

Amino acid targets of drug

116 ASN

270 ALA

273 ASP

90 ASP

No. of residues in known binding

18

Human similar targets

2

  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