Table 1.
Binding parameters for the interaction of HBV Pol with plant-derived antiviral compounds.
| Interacting Pol residues | Types of Interaction | Bond length (Å) |
|---|---|---|
| Lamivudine* | ||
| SER202:OG - UNK1:O | Hydrogen Bond | 3.00 |
| UNK1:C - ALA181:O | Carbon Hydrogen Bond | 3.51 |
| UNK1:C - ALA181:O | Carbon Hydrogen Bond | 3.66 |
| PRO59 - UNK1 | Hydrophobic (Alkyl) | 5.20 |
| ALA181 - UNK1 | Hydrophobic (Alkyl) | 5.12 |
| ALA181 - UNK1 | Hydrophobic (Alkyl) | 3.84 |
| UNK1 - PRO59 | Hydrophobic (Alkyl) | 4.42 |
| Quercetin | ||
| LYS32:HZ1 - UNK1:O | Hydrogen Bond | 2.87 |
| ASN36:HD21 - UNK1:O | Hydrogen Bond | 2.42 |
| ALA87:HN - UNK1:O | Hydrogen Bond | 2.24 |
| PHE88:HN - UNK1:O | Hydrogen Bond | 2.84 |
| UNK1:H - ASP83:OD1 | Hydrogen Bond | 2.57 |
| UNK1:H - ASP83:OD2 | Hydrogen Bond | 3.08 |
| UNK1:H - VAL84:O | Hydrogen Bond | 2.03 |
| LYS32:NZ - UNK1 | Electrostatic (Pi-Cation) | 4.30 |
| ARG41:NH2 - UNK1 | Electrostatic (Pi-Cation) | 3.54 |
| ASP83:OD2 - UNK1 | Electrostatic (Pi-Anion) | 3.74 |
| ARG41:HE - UNK1 | Hydrogen Bond | 3.04 |
| ALA86:HN - UNK1 | Hydrogen Bond | 3.12 |
| UNK1 - ARG41 | Hydrophobic (Pi-Alkyl) | 4.74 |
| UNK1 - MET171 | Hydrophobic (Pi-Alkyl) | 5.35 |
| Rutin | ||
| ASN36:ND2 - UNK1:O | Hydrogen Bond | 2.96 |
| ARG41:NH2 - UNK1:O | Hydrogen Bond | 3.13 |
| ASP83:N - UNK1:O | Hydrogen Bond | 3.17 |
| MET250:N - UNK1:O | Hydrogen Bond | 3.24 |
| GLY251:N - UNK1:O | Hydrogen Bond | 3.10 |
| UNK1:H - ASN248:O | Hydrogen Bond | 1.99 |
| UNK1:H - SER81:O | Hydrogen Bond | 1.79 |
| UNK1:H - ASN33:O | Hydrogen Bond | 2.53 |
| ASP83:OD2 - UNK1 | Electrostatic (Pi-Anion) | 4.46 |
| ASP83:OD2 - UNK1 | Electrostatic (Pi-Anion) | 4.49 |
| UNK1 - LYS241 | Hydrophobic (Pi-Alkyl) | 4.56 |
| Hesperidin | ||
| SER40:N - UNK1:O | Hydrogen Bond | 2.79 |
| SER40:OG - UNK1:O | Hydrogen Bond | 2.89 |
| SER85:OG - UNK1:O | Hydrogen Bond | 2.86 |
| SER117:OG - UNK1:O | Hydrogen Bond | 2.70 |
| UNK1:H - SER117:OG | Hydrogen Bond | 2.14 |
| UNK1:H - SER40:OG | Hydrogen Bond | 2.22 |
| UNK1:H - GLU39:OE2 | Hydrogen Bond | 1.98 |
| HIS156:CE1 - UNK1:O | Carbon Hydrogen Bond | 3.39 |
| TRP3 - UNK1 | Hydrophobic (Pi-Pi Stacked) | 5.28 |
| TRP3 - UNK1 | Hydrophobic (Pi-Pi Stacked) | 5.18 |
| UNK1:C - LEU147 | Hydrophobic (Alkyl) | 4.17 |
| UNK1 - ALA86 | Hydrophobic (Pi-Alkyl) | 5.23 |
| Lupeol | ||
| ARG120 - UNK1 | Hydrophobic (Alkyl) | 4.59 |
| UNK1:C - LEU42 | Hydrophobic (Alkyl) | 5.39 |
| UNK1:C - ARG120 | Hydrophobic (Alkyl) | 3.87 |
| UNK1:C - PRO5 | Hydrophobic (Alkyl) | 4.29 |
| TRP3 - UNK1:C | Hydrophobic (Pi-Alkyl) | 4.99 |
| HIS156 - UNK1 | Hydrophobic (Pi-Alkyl) | 5.22 |
| HIS156 - UNK1:C | Hydrophobic (Pi-Alkyl) | 4.59 |
| HIS156 - UNK1:C | Hydrophobic (Pi-Alkyl) | 5.19 |
| TYR158 - UNK1:C | Hydrophobic (Pi-Alkyl) | 5.20 |
| TYR158 - UNK1:C | Hydrophobic (Pi-Alkyl) | 4.83 |
| Azadirachtin | ||
| SER117:OG - UNK1:O | Hydrogen Bond | 2.97 |
| ARG120:NE - UNK1:O | Hydrogen Bond | 3.10 |
| ARG153:NH1 - UNK1:O | Hydrogen Bond | 2.82 |
| ARG153:NH1 - UNK1:O | Hydrogen Bond | 3.25 |
| UNK1:C - GLU1:OE2 | Carbon Hydrogen Bond | 3.52 |
| UNK1:C - PRO5 | Hydrophobic (Alkyl) | 4.37 |
| HIS156 - UNK1:C | Hydrophobic (Pi-Alkyl) | 4.77 |
| HIS156 - UNK1:C | Hydrophobic (Pi-Alkyl) | 5.08 |
| β-Sitosterol | ||
| UNK1:C - TRP3 | Hydrophobic (Pi-Sigma) | 3.98 |
| UNK1:C - ARG41 | Hydrophobic (Alkyl) | 3.95 |
| UNK1:C - MET171 | Hydrophobic (Alkyl) | 4.16 |
| UNK1:C - LEU42 | Hydrophobic (Alkyl) | 4.98 |
| UNK1:C - MET171 | Hydrophobic (Alkyl) | 5.19 |
| UNK1:C - PRO4 | Hydrophobic (Alkyl) | 4.05 |
| TRP3 - UNK1 | Hydrophobic (Pi-Alkyl) | 5.13 |
| TRP3 - UNK1:C | Hydrophobic (Pi-Alkyl) | 5.00 |
| TRP3 - UNK1 | Hydrophobic (Pi-Alkyl) | 4.05 |
| TRP3 - UNK1 | Hydrophobic (Pi-Alkyl) | 4.10 |
| TRP3 - UNK1:C | Hydrophobic (Pi-Alkyl) | 5.25 |
| PHE88 - UNK1:C | Hydrophobic (Pi-Alkyl) | 5.17 |
| TYR89 - UNK1:C | Hydrophobic (Pi-Alkyl) | 4.85 |
| TYR89 - UNK1:C | Hydrophobic (Pi-Alkyl) | 4.83 |
| HIS160 - UNK1:C | Hydrophobic (Pi-Alkyl) | 4.39 |
| HIS160 - UNK1:C | Hydrophobic (Pi-Alkyl) | 4.42 |
| Psoralen | ||
| LYS32:HZ3 - UNK1: O | Hydrogen Bond | 2.30 |
| ARG41: HE - UNK1:O | Hydrogen Bond | 2.48 |
| ARG41:HH22 - UNK1: O | Hydrogen Bond | 2.34 |
| HIS160:NE2 - UNK1 | Electrostatic (Pi-Cation) | 4.94 |
| HIS160 - UNK1 | Hydrophobic (Pi-Pi T-shaped) | 5.39 |
| UNK1 - ALA86 | Hydrophobic (Pi-Alkyl) | 5.17 |
| UNK1 - MET171 | Hydrophobic (Pi-Alkyl) | 5.22 |
| UNK1 - PRO5 | Hydrophobic (Pi-Alkyl) | 5.39 |
| UNK1 - ALA86 | Hydrophobic (Pi-Alkyl) | 4.76 |
| UNK1 - ALA86 | Hydrophobic (Pi-Alkyl) | 4.44 |
| Embelin | ||
| LYS32:HZ1 - UNK1: O | Hydrogen Bond | 2.70 |
| HIS160:HE2 - UNK1: O | Hydrogen Bond | 2.77 |
| HIS160:CE1 - UNK1: O | Carbon Hydrogen Bond | 3.34 |
| UNK1:C - PRO5 | Hydrophobic (Alkyl) | 4.25 |
| TRP3 - UNK1:C | Hydrophobic (Pi-Alkyl) | 4.73 |
| UNK1 - ARG41 | Hydrophobic (Pi-Alkyl) | 4.63 |
| UNK1 - ALA86 | Hydrophobic (Pi-Alkyl) | 5.18 |
| Menisdaurin | ||
| MET250:HN - UNK1:O | Hydrogen Bond | 2.85 |
| GLN267:HE21 - UNK1:O | Hydrogen Bond | 2.10 |
| UNK1:C - ASN248:O | Carbon Hydrogen Bond | 3.55 |
| LYS241 - UNK1 | Hydrophobic (Alkyl) | 4.52 |
| Baccatin III | ||
| ASN33:HD21 - UNK1:O | Hydrogen Bond | 2.33 |
| ASN36:HD21 - UNK1:O | Hydrogen Bond | 2.40 |
| UNK1:H - ASN248:O | Hydrogen Bond | 2.75 |
| LYS241:CE - UNK1:O | Carbon Hydrogen Bond | 3.62 |
| NK1:C - ASP83:OD2 | Carbon Hydrogen Bond | 3.38 |
| UNK1:C - MET250 | Hydrophobic (Alkyl) | 4.81 |
*
Standard/positive control.