Table 3.
Binding energies (kcal/mol) and binding modes of small-molecule ligands to receptors (LRRK2, NMDA, and TrkA).
| No. | Structure | ZINC Code | Binding Energy ΔG, kcal/mol | Ligand Efficiency | Binding Mode, Including H-Bonds (Residue of Amino Acid Group or Atom in a Compound) |
|---|---|---|---|---|---|
| NMDA | |||||
| GNE-5729 |
|
==== | −11.3 | −0.42 | Ile116, Val128, Pro129, Phe130, Pro141, Lys143, Tyr144, Thr242, Leu262, Leu263, Val266, Leu270 |
| 1N |
|
ZINC98363705 | −9.8 | −0.39 | Pro129, Phe130, Val131, Glu132, Pro141, Tyr144, Leu263, Val266, Met271, Glu275 |
| 2N |
|
ZINC67658347 | −9.7 | −0.40 | Ile128, Pro129, Val131, Glu132, Pro141, Tyr144, Thr242, Gly243, Gly250, Val266, His273 (N...HN) |
| 3N |
|
ZINC98364250 | −9.0 | −0.39 | Ile128, Pro129, Glu132, Pro141, Tyr144, Thr242, Gly250 (NH...N), Leu263, Val266 |
| LRRK2 | |||||
| PF-06447475 |
|
==== | −9.0 | −0.39 | Ile30, Glu31, Ala51, Lys53, Glu100 (O...HN), Leu102 (NH...N), Leu151, Asp162 |
| 1L |
|
ZINC2115150 | −9.0 | −0.36 | Ile30, Val38, Lys53, Glu70, Tyr101, Leu102, Asp162 |
| 2L |
|
ZINC12901845 | −8.5 | −0.37 | Leu102 (NH...O), Ser106 (HO....H2N), Gly105, Asp109, Leu151 |
| 3L |
|
ZINC518729 | −8.7 | −0.38 | Ile30, Val38, Tyr101, Leu102 (NH...OH), Gly105, Leu151 |
| TrkA | |||||
| AZ-23 |
|
ZINC35077985 | −8.7 | −0.32 | Leu516, Val524, Ala542, Phe589, Met592, Gly595, Asp596, Leu657 (O....HN) |
| 1T |
|
ZINC85880015 | −9.80 | −0.38 | Leu516, Gly519, Lys544, Phe589, Met592, Gly595, Leu657, Asp668 |
| 2T |
|
ZINC1323099 | −8.6 | −0.54 | Val524, Ala542, Phe589, Met592, Leu657 |
| 3T |
|
ZINC489632 | −9.5 | −0.38 | Leu516 (O... HO), Gly517, Ala542, Lys544, Phe589, Met592 (NH...O), Leu657, Gly667 |