Result table
Rank
| Est. Free Energy
of Binding | Est. Inhibition
Constant, Ki | vdW + Hbond
+ desolv Energy | Electrostatic
Energy | Total Intermolec.
Energy | Frequency
|
1 | -5.49 kcal/mol | 94.04 uM | -6.74 kcal/mol | -1.37 kcal/mol | -8.11 kcal/mol | 30 |
Interaction Table
hydrogen bonds | polar | hydrophobic | other |
|---|
O3 (19)
[3.15] | – | LYS101 (NZ) | | N2 (18)
[3.59] | – | LYS101 (NZ) | | C2 (2)
[3.20] | – | LEU99 (CB, CD2) | | H6 (32)
[3.40] | – | ALA120 (CB) | |
O4 (20)
[3.16] | – | LYS101 (NZ) | | N2 (18)
[3.72] | – | GLU177 (OE2) | | C18 (26)
[3.23] | – | LEU99 (CD1) | | C10 (13)
[2.63] | – | GLU177 (CD, OE2) | |
H12 (38)
[3.51] | – | LYS101 (NZ) | | O1 (3)
[3.81] | – | GLU177 (OE2) | | C14 (17)
[3.29] | – | VAL107 (CB, CG2) | | C8 (11)
[3.39] | – | GLU177 (OE2) | |
| | O6 (23)
[3.78] | – | GLU177 (OE2) | | C13 (16)
[3.16] | – | VAL107 (CB, CG2) | | C9 (12)
[3.38] | – | GLU177 (OE2) | |
| | | C17 (25)
[3.32] | – | LEU154 (CD2) | | C11 (14)
[3.59] | – | GLU177 (OE2) | |
| | | C17 (25)
[3.54] | – | LEU170 (CD1) | | C3 (4)
[3.84] | – | GLU177 (OE2) | |
| | | C18 (26)
[3.49] | – | PHE172 (CD1, CE1) | | O6 (23)
[3.55] | – | LEU223 (CD1, CD2, CG) | |
| | | C4 (6)
[3.84] | – | LEU223 (CD1) | | N1 (8)
[3.81] | – | LEU223 (CD1) | |
| | | C6 (9)
[3.47] | – | LEU223 (CD1) | | |
| | | C7 (10)
[3.37] | – | LEU223 (CD1) | | |
| | | C8 (11)
[3.69] | – | LEU223 (CD1, CD2) | | |
| | | C15 (21)
[3.82] | – | LEU223 (CD1) | | |
Docking calculations were carried out using DockingServer (
Bikadi, Hazai, 2009). The MMFF94 force field (
Halgren, 1998) was used for energy minimization of ligand molecule (
nitrendipine.pdb) using DockingServer. Gasteiger partial charges were added to the ligand atoms. Non-polar hydrogen atoms were merged, and rotatable bonds were defined.
Docking calculations were carried out on
2VGO.pdb protein model. Essential hydrogen atoms, Kollman united atom type charges, and solvation parameters were added with the aid of AutoDock tools (
Morris, Goodsell et al., 1998). Affinity (grid) maps of 20×20×20 Å grid points and 0.375 Å spacing were generated using the Autogrid program (
Morris, Goodsell et al., 1998). AutoDock parameter set- and distance-dependent dielectric functions were used in the calculation of the van der Waals and the electrostatic terms, respectively.
Docking simulations were performed using the Lamarckian genetic algorithm (LGA) and the Solis & Wets local search method (
Solis and Wets, 1981). Initial position, orientation, and torsions of the ligand molecules were set randomly. Each docking experiment was derived from 10 different runs that were set to terminate after a maximum of 250000 energy evaluations. The population size was set to 150. During the search, a translational step of 0.2 Å, and quaternion and torsion steps of 5 were applied.
