Table 3.
The binding details of polyphenols present in Geranii Herba (Geraniaceae) with 3C-like proteinase (3CLpro).
| Ligand | Protein PDB ID |
Binding Amino Acid Residues | Binding Energy (kcal/mol) |
Inhibition Constant μM |
VDW_HB Desolv_Energy (kcal/mol) |
Ligand Efficiency |
|---|---|---|---|---|---|---|
| Corilagin | 3CLpro (6LU7) |
THR26/HN/O, PHE140/O, HIS164/O, GLU166/HN/OE2, | −5.82 | 54.33 | −9.44 | 0.13 |
| Ellagic acid | 3CLpro (6LU7) |
LEU141/O, GLY143/HN, SER144/HN/HG, CYS145/HN, HIS163/HE2, GLU166/OE2/HN/O, HIS172/HE2, GLN189/OE1, | −6.37 | 21.54 | −7.18 | 0.29 |
| Gallic acid | 3CLpro (6LU7) |
LEU141/OGLY143/HN, SER144/HN, HIS163/HE2, GLU166/HN | −4.46 | 535.39 | −4.86 | 0.32 |
| Geraniin | 3CLpro (6LU7) |
PHE140/O, LEU141/O, HIS163/HE2, GLU166/HN, ARG188/O, GLN189/O, THR190/O, GLN192/1HE2 | −9.78 | 67.61 | −10.76 | 0.38 |
| Kaempferitrin | 3CLpro (6LU7) |
LEU141/O, ASN142/OD1, SER144/OG, HIS163/HE2, GLU166/O | −7.83 | 286.47 | −8.48 | 0.28 |
| Kaempferol7-O-rhamnoside | 3CLpro (6LU7) |
LEU141/O, SER144/HN, CYS145/HN, HIS163/HE2, PRO168/O | −5.87 | 49.91 | −8.42 | 0.19 |
| Kaempferol | 3CLpro (6LU7) |
GLY143/HN, SER144/N, GLU166/O/HN, ASP187/O | −7.76 | 2.04 | −9.14 | 0.36 |
| Protocatechuic acid | 3CLpro (6LU7) |
LEU141/O, GLY143/HN, SER144/HN, CYS145/HN, HIS163/HE2, GLU166/HN | −4.32 | 677.36 | −4.59 | 0.34 |
| Quercetin | 3CLpro (6LU7) |
LEU141/O, GLY143/HN, SER144/HN, GLU166/HN | −6.49 | 3.24 | −9.2 | 0.30 |