Table 1. Details of the docking results of 30 anti-AD targets with the number of successfully docked TCM compounds.
| RCSB ID | Protein name | Original ligands ID | Binding energy of original liganda | Lowest docking energy | Compound numberb |
|---|---|---|---|---|---|
| 1DB4 | PLA2(Phospholipase A2, membrane associated) | 8IN | −7.31 | −11.55 | 5,290 |
| 1DQA | HMG-COA(3-hydroxy-3-methylglutaryl-coenzyme A reductase) | NAP | −7.42 | −9.78 | 437 |
| 1NME | Caspase-3 | 159 | −4.57 | −10.24 | 21,028 |
| 1OJA | MAOB(Amine oxidase [flavin-containing] B) | ISN | −6.58 | −12.2 | 11,173 |
| 1TB7 | PDE4(cAMP-specific 3′,5′-cyclic phosphodiesterase 4D) | AMP | −6.47 | −14.5 | 17,375 |
| 1TN6 | Ftase(Protein farnesyltransferase subunit beta) | FII | −6.59 | −11.9 | 14,437 |
| 2AFW | QC(Glutaminyl-peptide cyclotransferase) | AHN | −4.48 | −11.11 | 23,635 |
| 2AZ5 | TNF(Tumor necrosis factor) | 307 | −5.66 | −9.53 | 9,261 |
| 2D0T | IDO(Indoleamine 2,3-dioxygenase 1) | PIM | −5.71 | −12.4 | 20,739 |
| 2DQ7 | Fyn(Tyrosine-protein kinase Fyn) | STU | −10.28 | −12.41 | 63 |
| 2VQM | HDAC(Histone deacetylase 4) | HA3 | −7.11 | −11.33 | 5,356 |
| 2Z5Y | MAOA(Amine oxidase [flavin-containing] A) | HRM | −7.96 | −12.8 | 5,299 |
| 3A4O | lyn(Tyrosine-protein kinase Lyn) | STU | −9.4 | −12.53 | 431 |
| 3G9N | JNK(Mitogen-activated protein kinase 10) | J88 | −7.19 | −10.36 | 1,606 |
| 3IKA | EGFR(Epidermal growth factor receptor) | 0UN | −7.64 | −11.45 | 6,324 |
| 3KMR | RAR(Retinoic acid receptor alpha) | EQN | −12.65 | −11.4 | 0 |
| 3O3U | RAGE(Advanced glycosylation end product-specific receptor) | MLR | −7.76 | −14.08 | 13,309 |
| 4DJU | BACE-1(Beta-secretase 1) | 0KK | −7.12 | −12.2 | 14,161 |
| 4EY5 | AchE(Acetylcholinesterase) | HUP | −8.5 | −10.6 | 329 |
| 4MS4 | GABA(B)(Gamma-aminobutyric acid type B receptor subunit 1) | 2C0 | −5.73 | −10.6 | 13,107 |
| 4OC7 | RXR(Retinoic acid receptor RXR-alpha) | 2QO | −8.48 | −11.3 | 708 |
| 4XAR | MGLUR(Metabotropic glutamate receptor 3) | 40F | −4.98 | −8.5 | 9,244 |
| 4YLK | DYRK1A(Dual specificity tyrosine-phosphorylation-regulated kinase 1A) | 4E2 | −8.13 | −12.54 | 7,167 |
| 4ZGM | GLP-1R(Glucagon-like peptide 1 receptor) | 32M | −3.31 | −9.06 | 24,782 |
| 4ZZJ | SIRT1(NAD-dependent protein deacetylase sirtuin-1) | 4TQ | −6.89 | −8.86 | 108 |
| 5A46 | FGFR1(Fibroblast growth factor receptor 1) | 38O | −8.54 | −12.8 | 699 |
| 5AFH | α7NACHR(Neuronal acetylcholine receptor subunit alpha-7) | L0B | −6.02 | −9.64 | 6,934 |
| 5H8S | AMPA(Glutamate receptor 2) | 5YC | −5.3 | −8.44 | 8,926 |
| 5HK1 | SIG-1R(Sigma non-opioid intracellular receptor 1) | 61W | −9.29 | −12.8 | 1,281 |
| 5IH5 | CKI-δ(Casein kinase I isoform delta) | AUE | −7.62 | −12.5 | 5,998 |
Notes.
a
‘Binding Energy of Original Ligand’ indicates the docking energy of the ligand embedded in the crystal structure.
b
The number of compounds with better docking scores than that of the original ligand embedded in the crystal structure.