DockingServer

Naltrexone to HMUR_crystal

Author: Dr. renyu liu - 13/08/07, 09:48

More docking results of Dr. renyu liu











Result table

Rank
 
Est. Free Energy
of Binding
Est. Inhibition
Constant, Ki
vdW + Hbond
+ desolv Energy
Electrostatic
Energy
Total Intermolec.
Energy
Frequency
 
1
-8.73 kcal/mol
399.16 nM
-9.18 kcal/mol
-1.16 kcal/mol
-10.34 kcal/mol
94
 





Interaction Table

hydrogen bonds
polar
hydrophobic
pi-pi
other
  N1 (5)
  [2.91]		 – ASP147 (CG, OD1, OD2)
  O2 (2)
  [2.87]		 – ASP147 (OD2)
  C6 (11)
  [3.65]		 – MET151 (SD)
  C16 (21)
  [3.72]		 – TRP293 (CH2)
  C8 (13)
  [3.24]		 – ASP147 (CG, OD2)
  H3 (28)
  [2.77]		 – ASP147 (OD2)
  H1 (26)
  [2.05]		 – ASP147 (OD2)
  C8 (13)
  [3.59]		 – MET151 (CE, SD)
  C17 (22)
  [3.70]		 – TRP293 (CH2)
  H1 (26)
  [3.28]		 – ASP147 (CG)
  H3 (28)
  [3.80]		 – TYR326 (OD2)
 
  C10 (15)
  [3.54]		 – MET151 (SD)
  C16 (21)
  [3.29]		 – TYR326 (CD1, CD2, CE1, CE2, CG, CZ)
  C11 (16)
  [3.68]		 – ASP147 (OD1, OD2)
   
  C18 (23)
  [3.54]		 – MET151 (SD)
  C13 (18)
  [3.54]		 – TYR326 (CE1, CE2, CZ)
  C5 (10)
  [3.35]		 – ASP147 (OD2)
   
  C20 (25)
  [3.74]		 – MET151 (SD)
 
  O4 (4)
  [3.74]		 – VAL236 (CG1)
   
  C5 (10)
  [3.62]		 – MET151 (CE)
 
  H2 (27)
  [3.36]		 – VAL236 (CG1)
   
  C9 (14)
  [3.76]		 – TRP293 (CZ3)
 
  C18 (23)
  [3.79]		 – HIS297 (ND1, NE2)
   
  C11 (16)
  [3.35]		 – TRP293 (CH2, CZ3)
 
  C20 (25)
  [3.13]		 – HIS297 (ND1, NE2)
   
  C9 (14)
  [3.76]		 – ILE296 (CG1)
 
  O4 (4)
  [3.61]		 – VAL300 (CB, CG1)
   
  C18 (23)
  [3.89]		 – ILE296 (CG2)
 
  H2 (27)
  [3.44]		 – VAL300 (CG1)
   
  C20 (25)
  [3.28]		 – HIS297 (CE1, CG)
 
  C13 (18)
  [3.89]		 – TYR326 (OH)
   
  C18 (23)
  [3.75]		 – HIS297 (CE1)
   
   
  C19 (24)
  [3.88]		 – VAL300 (CG2)
   
   
  C7 (12)
  [3.42]		 – ILE322 (CD1)
   
 








Docking calculations were carried out using DockingServer (Bikadi, Hazai, 2009). The MMFF94 force field (Halgren, 1998) was used for a preliminary energy minimization of ligand molecule (Naltrexone) using DockingServer. 0 semiempirical method was used in a second step to optimize the geometry of ligand molecule. 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 HMUR_crystal 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 30×30×30 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 100 different runs that were set to terminate after a maximum of 2500000 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.



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