Table 4.
Flexible docking results of various ligands to the S1-nAChR-α7-dimer complex (S1 bound to an α7 dimer) before and after MDS.
| Docking | After 20 ns MDS |
|||||
|---|---|---|---|---|---|---|
| Ligand | PDB code | Prot-Lig ΔG (Vina) [kcal/mol] | *S1 shift [Å] | #S1 RMSD [Å] | Prot-Lig ΔG (Vina) [kcal/mol] | S1−2α7 ΔG (Prodigy) [kcal/mol] |
| Acetylcholine (ach) | 3WIP | Model 1 −3.7 | 0.977 | 5.617 | −4.0 | −9.6 |
| Carbamylcholine (cce) | 1UV6 | Model 1 −3.8 | 1.756 | 4.569 | −4.0 | −10.4 |
| Cytisine (c5e) | 4BQT | Model 8 −7.8 | 0.611 | 2.958 | −8.5 | −12.4 |
| Epibatidine (epj) | 3SQ6 | Model 3 −7.5 | 0.244 | 4.746 | −7.4 | −11.5 |
| Galantamine (gnt) | 2PH9 | Model 1 −10.9 | 3.028 | 8.568 | −6.0 | −8.0 |
| Nicotine (nct) | 1UW6 | Model 6 −5.9 | 0.285 | 5.603 | −6.9 | −12.6 |
| Succinylcholine (sck) | 2HA2 | Model 2 −5.6 | 5.979 | 10.083 | −3.7 | −8.3 |
| Varenicline (qmr) | 4AFT | Model 8 −7.2 | 0.0512 | 3.971 | −8.7 | −13.1 |
| S1-2α7 complex, no ligand | 1.075 | 3.062 | −9.7 | |||
*
Shift of S1 geometrical center from 2α7 geometrical center after 20 ns MDS.
#
RMSD of S1 after MDS relative to its starting position without correction for translation and rotation. That is S1 RMSD includes conformational as well as positional changes.