Table 3 Result of best-performed ligand molecules in the IFD experiment, type of interactions, interacting amino acids, and bond distances
From: Computer-assisted evaluation of plant-derived β-secretase inhibitors in Alzheimer’s disease
Compound name | XP Gscore (Kcal/mol) | IFD score (Kcal/mol) | Interacting residues | Bond distance (Å) | Type of interaction | Interaction category |
|---|---|---|---|---|---|---|
Amentoflavone | − 7.842 | − 823.501 | Asp228 | 3.04 | Hydrogen bond | Conventional |
Phe108 | 1.88 | Hydrogen bond | Conventional | |||
Lys107 | 1.97 | Hydrogen bond | Conventional | |||
Phe108 | 5.58 | Pi–Pi stacked | Hydrophobic | |||
Tyr71 | 5.15 | Pi–Pi T-shaped | Hydrophobic | |||
Gly34 | 2.34 | Hydrogen bond | Conventional | |||
Tyr71 | 5.51 | Pi–Pi stacked | Hydrophobic | |||
Tyr71 | 4.61 | Pi–Pi T-shaped | Hydrophobic | |||
Bilobetin | − 7.417 | − 821.327 | Lys107 | 1.94 | Hydrogen bond | Conventional |
Phe108 | 1.86 | Hydrogen bond | Conventional | |||
Tyr71 | 4.84 | Pi–Pi stacked | Hydrophobic | |||
Phe108 | 5.68 | Pi–Pi T-shaped | Hydrophobic | |||
Tyr71 | 4.67 | Pi–Pi stacked | Hydrophobic | |||
Asp228 | 2.81 | Carbon hydrogen bond | Non-conventional | |||
Tyr71 | 5.14 | Pi–Pi stacked | Hydrophobic | |||
Gly34 | 2.69 | Carbon hydrogen bond | Non-conventional | |||
Tyr198 | 2.03 | Hydrogen bond | Conventional | |||
Ellagic acid | − 6.923 | − 819.500 | Tyr71 | 4.97 | Pi–Pi stacked | Hydrophobic |
Asp32 | 1.79 | Hydrogen bond | Conventional | |||
Tyr71 | 4.40 | Pi–Pi stacked | Hydrophobic | |||
Thr72 | 1.99 | Hydrogen bond | Conventional | |||
Tyr71 | 3.82 | Pi–Pi stacked | Hydrophobic | |||
Thr72 | 2.01 | Hydrogen bond | Conventional | |||
Tyr71 | 3.93 | Pi–Pi stacked | Hydrophobic |