DockingServer

<b>Nadolol</b> (JP15/USP/INN) to 3dlw - HYDROLASE INHIBITOR

Author: Prudvi Kalyan - 10/08/07, 00:24

More docking results of Prudvi Kalyan









Result table

Rank
 
Est. Free Energy
of Binding
Est. Inhibition
Constant, Ki
vdW + Hbond
+ desolv Energy
Electrostatic
Energy
Total Intermolec.
Energy
Frequency
 
1
+285.03 kcal/mol
+283.12 kcal/mol
-0.09 kcal/mol
+283.03 kcal/mol
10
 





Interaction Table

hydrophobic
pi-pi
cation-pi
other
  C4 ()
  [2.76]		 – PHE33 (CB, CD1, CD2, CE2, CG, CZ)
  C5 ()
  [2.16]		 – PHE33 (CD1, CD2, CE1, CE2, CG, CZ)
  H2 ()
  [3.45]		 – PHE33 (CD2)
  O2 ()
  [3.59]		 – PHE33 (CD2)
  C2 ()
  [2.49]		 – PHE33 (CD2, CE2, CG)
  C6 ()
  [2.50]		 – PHE33 (CD1, CD2, CE1, CE2, CG, CZ)
  H1 ()
  [2.00]		 – PHE52 (CD2, CE2, CZ)
  O3 ()
  [2.94]		 – PHE33 (CE2, CZ)
  C1 ()
  [3.05]		 – PHE33 (CD2, CE2)
  C9 ()
  [2.73]		 – PHE33 (CD1, CD2, CE1, CE2, CG, CZ)
 
  O2 ()
  [2.66]		 – ALA34 (CB)
  C3 ()
  [2.34]		 – PHE33 (CD2, CE2, CZ)
  C14 ()
  [2.65]		 – PHE33 (CD1, CE1, CE2, CZ)
 
  H2 ()
  [2.49]		 – ALA34 (CB)
  C4 ()
  [2.81]		 – LEU37 (CB, CD2, CG)
  C7 ()
  [2.21]		 – PHE33 (CE1, CE2, CZ)
 
  O1 ()
  [2.72]		 – LEU37 (CD2, CG)
  C5 ()
  [1.92]		 – LEU37 (CB, CD1, CD2, CG)
  C13 ()
  [2.57]		 – PHE33 (CE1, CE2, CZ)
 
  O3 ()
  [3.09]		 – LEU37 (CD1, CD2)
  C6 ()
  [2.41]		 – LEU37 (CB, CD1, CD2, CG)
   
  H1 ()
  [3.56]		 – LEU37 (CD2)
  C7 ()
  [2.39]		 – LEU37 (CB, CD1, CD2, CG)
   
  O1 ()
  [2.34]		 – PHE52 (CD2, CE2, CZ)
  C9 ()
  [2.26]		 – LEU37 (CB, CD1, CD2, CG)
   
  O1 ()
  [2.94]		 – PRO54 (CB)
  C13 ()
  [2.51]		 – LEU37 (CB, CD1, CD2, CG)
   
  H1 ()
  [2.19]		 – PRO54 (CB, CD, CG)
  C14 ()
  [2.57]		 – LEU37 (CB, CD1, CD2, CG)
   
  O2 ()
  [2.10]		 – PRO54 (CB, CG)
  C3 ()
  [2.46]		 – LEU37 (CD2, CG)
   
  H2 ()
  [2.52]		 – PRO54 (CB, CG)
  C12 ()
  [3.34]		 – LEU37 (CD1, CD2)
   
  O3 ()
  [2.10]		 – ILE57 (CB, CD1, CG1, CG2)
  C1 ()
  [3.03]		 – LEU37 (CD2)
   
  N1 ()
  [3.68]		 – ILE57 (CG2)
  C2 ()
  [3.70]		 – LEU37 (CD2)
   
  O1 ()
  [3.22]		 – ILE57 (CD1)
  C1 ()
  [3.75]		 – PHE52 (CE2)
   
  N1 ()
  [3.18]		 – LEU61 (CD1, CD2, CG)
  C1 ()
  [3.03]		 – PRO54 (CB)
   
  H4 ()
  [2.35]		 – LEU61 (CD1, CD2, CG)
  C2 ()
  [3.08]		 – PRO54 (CB)
   
  C15 ()
  [2.15]		 – THR165 (CB, OG1)
  C1 ()
  [3.46]		 – ILE57 (CB, CD1)
   
  C8 ()
  [3.28]		 – THR165 (OG1)
  C3 ()
  [2.67]		 – ILE57 (CB, CD1, CG1, CG2)
   
  C17 ()
  [3.40]		 – THR165 (OG1)
  C5 ()
  [3.43]		 – ILE57 (CB, CD1, CG2)
   
  O4 ()
  [2.50]		 – LEU301 (CB, CD1, CG)
  C11 ()
  [2.39]		 – ILE57 (CB, CG2)
   
  H3 ()
  [1.91]		 – LEU301 (CB, CD1, CG)
  C7 ()
  [3.14]		 – ILE57 (CG2)
   
  H5 ()
  [3.57]		 – LEU301 (CB, CD1)
  C12 ()
  [2.94]		 – ILE57 (CD1, CG2)
   
  O3 ()
  [3.73]		 – LEU301 (CD1)
  C10 ()
  [3.04]		 – ILE57 (CG2)
   
  O4 ()
  [2.17]		 – LEU305 (CB, CD1, CD2, CG)
  C17 ()
  [3.47]		 – ILE57 (CG2)
   
  H3 ()
  [2.50]		 – LEU305 (CD1, CD2, CG)
  C17 ()
  [3.12]		 – ALA60 (CB)
   
  H4 ()
  [2.63]		 – LEU305 (CD1, CD2, CG)
  C11 ()
  [3.48]		 – LEU61 (CD1, CD2, CG)
   
  H5 ()
  [2.70]		 – LEU305 (CD1, CG)
  C8 ()
  [3.38]		 – LEU61 (CD2, CG)
   
  N1 ()
  [3.10]		 – LEU305 (CD1)
  C17 ()
  [3.03]		 – LEU61 (CD2, CG)
   
  O3 ()
  [3.50]		 – LEU305 (CD2)
  C16 ()
  [3.14]		 – LEU61 (CD2)
   
  H3 ()
  [2.98]		 – VAL334 (CB, CG1)
  C12 ()
  [2.54]		 – LEU301 (CB, CD1, CD2, CG)
   
  N1 ()
  [2.49]		 – VAL334 (CB, CG1, CG2)
  C10 ()
  [2.13]		 – LEU301 (CB, CD1, CG)
   
  H4 ()
  [3.09]		 – VAL334 (CB, CG1, CG2)
  C11 ()
  [3.38]		 – LEU301 (CD1)
   
  H5 ()
  [1.83]		 – VAL334 (CB, CG1, CG2)
  C12 ()
  [3.46]		 – LEU305 (CD2, CG)
   
  O4 ()
  [3.61]		 – VAL334 (CG1)
  C10 ()
  [3.35]		 – LEU305 (CD1, CD2, CG)
     
  C11 ()
  [3.45]		 – LEU305 (CD1, CD2)
     
  C7 ()
  [3.80]		 – LEU305 (CD2)
     
  C13 ()
  [3.20]		 – LEU305 (CD2)
     
  C9 ()
  [3.27]		 – LEU308 (CD1)
     
  C13 ()
  [3.58]		 – LEU308 (CD1)
     
  C14 ()
  [2.53]		 – LEU308 (CD1)
     
  C8 ()
  [2.42]		 – VAL334 (CB, CG1, CG2)
     
  C15 ()
  [2.10]		 – VAL334 (CB, CG1)
     
  C16 ()
  [2.65]		 – VAL334 (CB, CG1, CG2)
     
  C10 ()
  [3.79]		 – VAL334 (CG1)
     
  C11 ()
  [3.69]		 – VAL334 (CG1)
     
 









Docking calculations were carried out using DockingServer (Bikadi, Hazai, 2009). 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 Nadolol (JP15/USP/INN) 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 ×× 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. All rotatable torsions were released during docking. 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.





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