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. 2018 May 11;6:e4756. doi: 10.7717/peerj.4756

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.