Table 2.
Interaction analysis of the best compounds that exhibited high docking score with AURKA, CDK1 and VEGFR target proteins
| Protein name | Compound name | Binding affinity (kcal/mol) |
No. of bonds | Types of bonds | Interacting residues | Bond length (Å) |
|---|---|---|---|---|---|---|
| AURKA | 3-Benzoyl-2,4(1H,3H)-Pyrimidinedione | – 8.0 | 7 | Hydrophobic bond | LEU139 | 3.53 |
| Hydrophobic bond | VAL147 | 3.99 | ||||
| Hydrophobic bond | ALA160 | 3.85 | ||||
| Hydrophobic bond | TYR212 | 3.60 | ||||
| Hydrophobic bond | LEU263 | 3.86 | ||||
| Hydrophobic bond | ALA273 | 3.94 | ||||
| Hydrogen bond | GLU260 | 2.38 | ||||
| Alpha-Curcumene | – 8.0 | 9 | Hydrophobic bond | LEU139 | 3.69 | |
| Hydrophobic bond | VAL147 | 3.79 | ||||
| Hydrophobic bond | ALA160 | 3.77 | ||||
| Hydrophobic bond | LYS162 | 3.63 | ||||
| Hydrophobic bond | LEU196 | 3.75 | ||||
| Hydrophobic bond | LEU208 | 3.99 | ||||
| Hydrophobic bond | LEU210 | 3.63 | ||||
| Hydrophobic bond | LEU263 | 3.70 | ||||
| Hydrophobic bond | PHE275 | 3.72 | ||||
| 8-Benzoyloctanoic acid | – 7.5 | 9 | Hydrophobic bond | LEU139 | 3.73 | |
| Hydrophobic bond | ALA160 | 3.70 | ||||
| Hydrophobic bond | LEU194 | 3.79 | ||||
| Hydrophobic bond | LEU196 | 3.47 | ||||
| Hydrophobic bond | LEU208 | 3.74 | ||||
| Hydrophobic bond | LEU210 | 3.65 | ||||
| Hydrogen bond | ALA213 | 3.01 | ||||
| Hydrophobic bond | ALA273 | 3.86 | ||||
| Hydrophobic bond | PHE273 | 3.60 | ||||
| CDK1 | 1-Cyclohexylethanol, trifluoroacetate | – 6.3 | 7 | Hydrophobic bond | ILE10 | 3.58 |
| Hydrogen bonds | GLU12 | 3.95 | ||||
| Hydrophobic bond | VAL18 | 3.78 | ||||
| Salt bridge | LYS33 | 3.99 | ||||
| Hydrophobic bond | ASP86 | 3.70 | ||||
| Hydrogen bonds | ASN133 | 3.13 | ||||
| Hydrophobic bond | LEU135 | 3.79 | ||||
| 3-Benzoyl-2,4(1H,3H)-Pyrimidinedione | – 6.0 | 6 | Hydrophobic bond | ARG127 | 3.53 | |
| Hydrogen bond | ARG170 | 2.45 | ||||
| Hydrophobic bond | VAL174 | 3.21 | ||||
| π-Stacking | TYR181 | 4.79 | ||||
| Hydrophobic bond | VAL185 | 3.83 | ||||
| Hydrogen bond | GLU209 | 2.96 | ||||
| (2,4,6-Trimethylcyclohexyl) methanol | – 5.9 | 5 | Hydrophobic bond | ILE10 | 3.61 | |
| Hydrophobic bond | VAL18 | 3.68 | ||||
| Hydrophobic bond | LEU83 | 3.87 | ||||
| Hydrogen bond | ASP86 | 2.39 | ||||
| Hydrophobic bond | LEU135 | 3.72 | ||||
| VEGFR2 | Alpha-Curcumene | – 8.9 | 10 | Hydrophobic bond | LEU840 | 3.66 |
| Hydrophobic bond | VAL848 | 3.66 | ||||
| Hydrophobic bond | ALA866 | 3.56 | ||||
| Hydrophobic bond | LYS868 | 3.71 | ||||
| Hydrophobic bond | LEU889 | 3.63 | ||||
| Hydrophobic bond | VAL914 | 3.80 | ||||
| Hydrophobic bond | VAL916 | 3.52 | ||||
| Hydrophobic bond | PHE918 | 3.69 | ||||
| Hydrophobic bond | LEU1035 | 3.55 | ||||
| Hydrophobic bond | PHE1047 | 3.49 | ||||
| 8-Benzoyloctanoic acid | – 7.9 | 10 | Hydrophobic bond | LEU840 | 3.61 | |
| Hydrophobic bond | VAL848 | 3.27 | ||||
| Hydrophobic bond | ALA866 | 3.96 | ||||
| Salt bridge | LYS868 | 4.22 | ||||
| Hydrophobic bond | LEU889 | 3.48 | ||||
| Hydrophobic bond | VAL916 | 3.71 | ||||
| Hydrophobic bond | PHE918 | 3.67 | ||||
| Hydrophobic bond | LEU1035 | 3.91 | ||||
| Hydrogen bond | ASP1046 | 2.21 | ||||
| Hydrophobic bond | PHE1047 | 3.70 | ||||
| 9-Undecenoic acid, 2,6,10-trimethyl | – 7.6 | 9 | Hydrophobic bond | LEU840 | 3.52 | |
| Hydrophobic bond | LYS868 | 3.73 | ||||
| Hydrophobic bond | LEU889 | 3.45 | ||||
| Hydrophobic bond | VAL899 | 3.94 | ||||
| Hydrophobic bond | VAL914 | 3.79 | ||||
| Hydrophobic bond | VAL916 | 3.64 | ||||
| Hydrogen bond | CYS919 | 2.31 | ||||
| Hydrophobic bond | LEU1035 | 3.63 | ||||
| Hydrophobic bond | PHE1047 | 3.60 |