UTF-8
Drug Design: Kinases
253255231
Protein Kinase Example: Ligand Bonding and Drug Design
page 6 of 6
4.0
1
16true
1
18true
1
18true
1
org.concord.modeler.PageTextBox
600.0
290.0
<html>
<head>
</head>
<body marginwidth="10" marginheight="10">
<font face="Verdana, Arial, Helvetica, sans-serif" size="5">In order for
kinases to function they need to hold onto both an ATP molecule and a
target molecule for receiving a phosphate from ATP.</font>
<p>
<font face="Verdana, Arial, Helvetica, sans-serif" size="5">Both
hydrophobic (non-polar) and hydrophilic (polar) forces are utilized.</font>
</p>
<p>
<font face="Verdana, Arial, Helvetica, sans-serif" size="5">If a
particular kinase is causing a disease like cancer, one way to halt the
disease is to design a molecule that will block ATP or the phosphate
receiver from being able to dock with the kinase. To design such a
molecule we need to study how this particular kinase attaches to other
molecules. </font>
</p>
</body>
</html>
-392113
Raised Bevel
1
1
org.concord.modeler.text.LineIcon710.0305515<html><body align="center"><strong><font size="5" face="Verdana, Arial, Helvetica, sans-serif" color="rgb(051, 051, 051)">Binding of ATP and cAMP Dependent Kinase</font></strong></body></html>-46544255
1
1
org.concord.modeler.PageMolecularViewer
falsefalsefalse1ATP.pdbdrugPage6$0.jms500
500
Lowered Bevel
org.concord.modeler.PageTextBox
240.0
510.0
<html>
<head>
</head>
<body marginwidth="10" marginheight="10">
<form action="" name="form1" method="post" id="form1">
<table border="0" width="200">
<tr>
<td colspan="2">
<font face="Verdana, Arial, Helvetica, sans-serif" size="4"><strong>Explore
how ATP is bound to kinase</strong> by using the buttons below to
view the hydrophobic and hydrophilic interactions. </font>
</td>
</tr>
<tr>
<td align="center" colspan="2">
<input name="Submit" type="submit" script="
script:jmol:1:
exit;
connect (all) (all) hbond delete;
select image all;
remove;
moveto 2 { -319 101 942 12.8} 779.4 0.0 0.0 {10.506192 9.569129 1.502968} 38.3;
#add image pocket.gif (10,10);
select ATP;
center selected;
select all;
slab off;
spin off;
halos off;
hbonds off;
labels off;
cartoons off;
isosurface on;
hbonds off;
select ~core;
spacefill off;
wireframe off;
select ~bondedWater
label water
set labelalignment center
color labels black
select mn
label magnesium
set labelalignment center
color labels purple
select atomno=2966
label ATP
set labelalignment center
color labels yellow
" value="return to original view">
</td>
</tr>
<tr>
<td align="center" colspan="2">
<strong><font face="Verdana, Arial, Helvetica, sans-serif" size="3">Hydrophobic
interactions:</font></strong><font face="Verdana, Arial, Helvetica, sans-serif" size="3">
</font>
</td>
</tr>
<tr>
<td align="center">
<input name="Submit2" type="submit" script="
script:jmol:1:
exit;
connect (all) (all) hbond delete;
select image all;
remove;
#add image phobicOne.gif (10,10);
select all;
slab off;
spin off;
halos off;
hbonds off;
labels off;
cartoons on;
color cartoons group;
hbonds off;
select ~core;
spacefill off;
wireframe off;
isosurface off;
delay 1;
moveto 2 { 769 588 251 28.4} 3436.7 0.0 0.0 {6.6799994 7.208556 3.553278} 38.1;
select atp
define ~target selected
select 173:E
define ~non_target selected
select (~non_target and (carbon,sulfur,selenium) and within(4.5, (~target and (carbon,sulfur,selenium))))
define ~nontarget_phobic selected
define ~aas within(group,~nontarget_phobic)
select (~target and (carbon,sulfur,selenium) and within(4.5, (~non_target and (carbon,sulfur,selenium))))
define ~target_phobic selected
select ~target_phobic or ~nontarget_phobic
define ~all_phobic selected
center 173:E or (atp and carbon);
#-------------------- grow sidechains
set hermitelevel 0
define new1 *.CA and ~aas
define new2 *.CB and ~aas
select (*.CA or *.CB) #necessary for bonds between sidechain and backbone
select new1 or new2
delay 0.025
wireframe 10
select new2
spacefill 4%
select new1 or new2
delay 0.025
wireframe 20
select new2
spacefill 8%
select new1 or new2
delay 0.025
wireframe 30
select new2
spacefill 12%
select new1 or new2
delay 0.025
wireframe 40
select new2
spacefill 16%
select new1 or new2
delay 0.025
wireframe 50
select new2
spacefill 20%
define old *.CA and ~aas
define new1 *.CB and ~aas
define new2 within(2.0,new1) and not old and not new1
select new1 or new2
delay 0.025
wireframe 10
select new2
spacefill 4%
select new1 or new2
delay 0.025
wireframe 20
select new2
spacefill 8%
select new1 or new2
delay 0.025
wireframe 30
select new2
spacefill 12%
select new1 or new2
delay 0.025
wireframe 40
select new2
spacefill 16%
select new1 or new2
delay 0.025
wireframe 50
select new2
spacefill 20%
define old new1
define new1 new2
define new2 within(2.0,new1) and not old and not new1
select new1 or new2
delay 0.025
wireframe 10
select new2
spacefill 4%
select new1 or new2
delay 0.025
wireframe 20
select new2
spacefill 8%
select new1 or new2
delay 0.025
wireframe 30
select new2
spacefill 12%
select new1 or new2
delay 0.025
wireframe 40
select new2
spacefill 16%
select new1 or new2
delay 0.025
wireframe 50
select new2
spacefill 20%
define old new1
define new1 new2
define new2 within(2.0,new1) and not old and not new1
select new1 or new2
delay 0.025
wireframe 10
select new2 and not backbone #makes second connection to backbone for proline but doesn't spacefill the backbone atom
spacefill 4%
select new1 or new2
delay 0.025
wireframe 20
select new2 and not backbone
spacefill 8%
select new1 or new2
delay 0.025
wireframe 30
select new2 and not backbone
spacefill 12%
select new1 or new2
delay 0.025
wireframe 40
select new2 and not backbone
spacefill 16%
select new1 or new2
delay 0.025
wireframe 50
select new2 and not backbone
spacefill 20%
define old new1
define new1 new2
define new2 within(2.0,new1) and not old and not new1 and not backbone #stop extending proline
select new1 or new2
delay 0.025
wireframe 10
select new2
spacefill 4%
select new1 or new2
delay 0.025
wireframe 20
select new2
spacefill 8%
select new1 or new2
delay 0.025
wireframe 30
select new2
spacefill 12%
select new1 or new2
delay 0.025
wireframe 40
select new2
spacefill 16%
select new1 or new2
delay 0.025
wireframe 50
select new2
spacefill 20%
define old new1
define new1 new2
define new2 within(2.0,new1) and not old and not new1 and not backbone
select new1 or new2
delay 0.025
wireframe 10
select new2
spacefill 4%
select new1 or new2
delay 0.025
wireframe 20
select new2
spacefill 8%
select new1 or new2
delay 0.025
wireframe 30
select new2
spacefill 12%
select new1 or new2
delay 0.025
wireframe 40
select new2
spacefill 16%
select new1 or new2
delay 0.025
wireframe 50
select new2
spacefill 20%
# end grow sidechain code
set hermitelevel 4;
connect 4.5 (~target_phobic) (~nontarget_phobic) hbond modifyOrCreate
select all
hbonds 0.1
color hbond lightgreen;
" value="1 Example">
</td>
<td align="center">
<input name="Submit9" type="submit" script="
script:jmol:1:
exit;
connect (all) (all) hbond delete;
select image all;
remove;
#add image phobicAll.gif (10,10);
select all;
slab off;
spin off;
halos off;
hbonds off;
labels off;
cartoons on;
color cartoons group;
hbonds off;
select ~core;
spacefill off;
wireframe off;
isosurface off;
delay 1;
moveto 2 { 404 881 244 23.7} 786.9 0.0 0.0 {9.00922 9.745092 2.718593} 39.2;
select atp
define ~target selected
select not selected and not solvent
define ~non_target selected
select (~non_target and (carbon,sulfur,selenium) and within(4.5, (~target and (carbon,sulfur,selenium))))
define ~nontarget_phobic selected
define ~aas within(group,~nontarget_phobic)
select (~target and (carbon,sulfur,selenium) and within(4.5, (~non_target and (carbon,sulfur,selenium))))
define ~target_phobic selected
select ~target_phobic or ~nontarget_phobic
define ~all_phobic selected
center atp or selected;
#-------------------- grow sidechains
set hermitelevel 0
define new1 *.CA and ~aas
define new2 *.CB and ~aas
select (*.CA or *.CB) #necessary for bonds between sidechain and backbone
select new1 or new2
delay 0.025
wireframe 10
select new2
spacefill 4%
select new1 or new2
delay 0.025
wireframe 20
select new2
spacefill 8%
select new1 or new2
delay 0.025
wireframe 30
select new2
spacefill 12%
select new1 or new2
delay 0.025
wireframe 40
select new2
spacefill 16%
select new1 or new2
delay 0.025
wireframe 50
select new2
spacefill 20%
define old *.CA and ~aas
define new1 *.CB and ~aas
define new2 within(2.0,new1) and not old and not new1
select new1 or new2
delay 0.025
wireframe 10
select new2
spacefill 4%
select new1 or new2
delay 0.025
wireframe 20
select new2
spacefill 8%
select new1 or new2
delay 0.025
wireframe 30
select new2
spacefill 12%
select new1 or new2
delay 0.025
wireframe 40
select new2
spacefill 16%
select new1 or new2
delay 0.025
wireframe 50
select new2
spacefill 20%
define old new1
define new1 new2
define new2 within(2.0,new1) and not old and not new1
select new1 or new2
delay 0.025
wireframe 10
select new2
spacefill 4%
select new1 or new2
delay 0.025
wireframe 20
select new2
spacefill 8%
select new1 or new2
delay 0.025
wireframe 30
select new2
spacefill 12%
select new1 or new2
delay 0.025
wireframe 40
select new2
spacefill 16%
select new1 or new2
delay 0.025
wireframe 50
select new2
spacefill 20%
define old new1
define new1 new2
define new2 within(2.0,new1) and not old and not new1
select new1 or new2
delay 0.025
wireframe 10
select new2 and not backbone #makes second connection to backbone for proline but doesn't spacefill the backbone atom
spacefill 4%
select new1 or new2
delay 0.025
wireframe 20
select new2 and not backbone
spacefill 8%
select new1 or new2
delay 0.025
wireframe 30
select new2 and not backbone
spacefill 12%
select new1 or new2
delay 0.025
wireframe 40
select new2 and not backbone
spacefill 16%
select new1 or new2
delay 0.025
wireframe 50
select new2 and not backbone
spacefill 20%
define old new1
define new1 new2
define new2 within(2.0,new1) and not old and not new1 and not backbone #stop extending proline
select new1 or new2
delay 0.025
wireframe 10
select new2
spacefill 4%
select new1 or new2
delay 0.025
wireframe 20
select new2
spacefill 8%
select new1 or new2
delay 0.025
wireframe 30
select new2
spacefill 12%
select new1 or new2
delay 0.025
wireframe 40
select new2
spacefill 16%
select new1 or new2
delay 0.025
wireframe 50
select new2
spacefill 20%
define old new1
define new1 new2
define new2 within(2.0,new1) and not old and not new1 and not backbone
select new1 or new2
delay 0.025
wireframe 10
select new2
spacefill 4%
select new1 or new2
delay 0.025
wireframe 20
select new2
spacefill 8%
select new1 or new2
delay 0.025
wireframe 30
select new2
spacefill 12%
select new1 or new2
delay 0.025
wireframe 40
select new2
spacefill 16%
select new1 or new2
delay 0.025
wireframe 50
select new2
spacefill 20%
# end grow sidechain code
set hermitelevel 4;
connect 4.5 (~target_phobic) (~nontarget_phobic) hbond modifyOrCreate
select all
hbonds 0.1
color hbond lightgreen;
" value="show all">
</td>
</tr>
<tr>
<td align="center" colspan="2">
<strong><font face="Verdana, Arial, Helvetica, sans-serif" size="3">Hydrogen
bond between ATP and kinase:</font></strong><font face="Verdana, Arial, Helvetica, sans-serif" size="3">
</font>
</td>
</tr>
<tr>
<td align="center">
<input name="Submit3" type="submit" script="
script:jmol:1:
exit;
connect (all) (all) hbond delete;
select image all;
remove;
#add image hbondOne.gif (10,10);
select all;
slab off;
spin off;
halos off;
hbonds off;
labels off;
cartoons on;
color cartoons group;
hbonds off;
select ~core;
spacefill off;
wireframe off;
isosurface off;
delay 1;
moveto 2.0 { -53 -987 151 28.7} 1081.2 0.0 0.0 {16.1865 5.7125006 -0.243} 37.9;
select atp
define ~target selected
select 168:E
define ~non_target selected
select (~non_target and (oxygen, nitrogen) and within(3.5, (~target and (oxygen, nitrogen))))
define ~nontarget_hbonders selected
define ~aas within(group,~nontarget_hbonders)
select (~target and (oxygen, nitrogen) and within(3.5, (~non_target and (oxygen, nitrogen))))
define ~target_hbonders selected
select ~target_hbonders or ~nontarget_hbonders
define ~all_hbonders selected
center (atomno=1279 or atomno=2939);
#-------------------- grow sidechains
set hermitelevel 0
define new1 *.CA and ~aas
define new2 *.CB and ~aas
select (*.CA or *.CB) #necessary for bonds between sidechain and backbone
select new1 or new2
delay 0.025
wireframe 10
select new2
spacefill 4%
select new1 or new2
delay 0.025
wireframe 20
select new2
spacefill 8%
select new1 or new2
delay 0.025
wireframe 30
select new2
spacefill 12%
select new1 or new2
delay 0.025
wireframe 40
select new2
spacefill 16%
select new1 or new2
delay 0.025
wireframe 50
select new2
spacefill 20%
define old *.CA and ~aas
define new1 *.CB and ~aas
define new2 within(2.0,new1) and not old and not new1
select new1 or new2
delay 0.025
wireframe 10
select new2
spacefill 4%
select new1 or new2
delay 0.025
wireframe 20
select new2
spacefill 8%
select new1 or new2
delay 0.025
wireframe 30
select new2
spacefill 12%
select new1 or new2
delay 0.025
wireframe 40
select new2
spacefill 16%
select new1 or new2
delay 0.025
wireframe 50
select new2
spacefill 20%
define old new1
define new1 new2
define new2 within(2.0,new1) and not old and not new1
select new1 or new2
delay 0.025
wireframe 10
select new2
spacefill 4%
select new1 or new2
delay 0.025
wireframe 20
select new2
spacefill 8%
select new1 or new2
delay 0.025
wireframe 30
select new2
spacefill 12%
select new1 or new2
delay 0.025
wireframe 40
select new2
spacefill 16%
select new1 or new2
delay 0.025
wireframe 50
select new2
spacefill 20%
define old new1
define new1 new2
define new2 within(2.0,new1) and not old and not new1
select new1 or new2
delay 0.025
wireframe 10
select new2 and not backbone #makes second connection to backbone for proline but doesn't spacefill the backbone atom
spacefill 4%
select new1 or new2
delay 0.025
wireframe 20
select new2 and not backbone
spacefill 8%
select new1 or new2
delay 0.025
wireframe 30
select new2 and not backbone
spacefill 12%
select new1 or new2
delay 0.025
wireframe 40
select new2 and not backbone
spacefill 16%
select new1 or new2
delay 0.025
wireframe 50
select new2 and not backbone
spacefill 20%
define old new1
define new1 new2
define new2 within(2.0,new1) and not old and not new1 and not backbone #stop extending proline
select new1 or new2
delay 0.025
wireframe 10
select new2
spacefill 4%
select new1 or new2
delay 0.025
wireframe 20
select new2
spacefill 8%
select new1 or new2
delay 0.025
wireframe 30
select new2
spacefill 12%
select new1 or new2
delay 0.025
wireframe 40
select new2
spacefill 16%
select new1 or new2
delay 0.025
wireframe 50
select new2
spacefill 20%
define old new1
define new1 new2
define new2 within(2.0,new1) and not old and not new1 and not backbone
select new1 or new2
delay 0.025
wireframe 10
select new2
spacefill 4%
select new1 or new2
delay 0.025
wireframe 20
select new2
spacefill 8%
select new1 or new2
delay 0.025
wireframe 30
select new2
spacefill 12%
select new1 or new2
delay 0.025
wireframe 40
select new2
spacefill 16%
select new1 or new2
delay 0.025
wireframe 50
select new2
spacefill 20%
# end grow sidechain code
set hermitelevel 4;
connect 3.5 (~target_hbonders) (~nontarget_hbonders) hbond modifyOrCreate
select all
hbonds 0.15
color hbond violet;
" value="1 Example">
</td>
<td align="center">
<input name="Submit10" type="submit" script="
script:jmol:1:
exit;
connect (all) (all) hbond delete;
select image all;
remove;
#add image hbondAll.gif (10,10);
select all;
slab off;
spin off;
halos off;
hbonds off;
labels off;
cartoons on;
color cartoons group;
hbonds off;
select ~core;
spacefill off;
wireframe off;
isosurface off;
delay 1;
moveto 2.0 { -315 -921 231 34.0} 668.7 0.0 0.0 {11.070519 9.253871 1.1515654} 37.9;
select atp
define ~target selected
select not selected and not solvent
define ~non_target selected
select (~non_target and (oxygen, nitrogen) and within(3.5, (~target and (oxygen, nitrogen))))
define ~nontarget_hbonders selected
define ~aas within(group,~nontarget_hbonders)
select (~target and (oxygen, nitrogen) and within(3.5, (~non_target and (oxygen, nitrogen))))
define ~target_hbonders selected
select ~target_hbonders or ~nontarget_hbonders
define ~all_hbonders selected
center atp or selected;
#-------------------- grow sidechains
set hermitelevel 0
define new1 *.CA and ~aas
define new2 *.CB and ~aas
select (*.CA or *.CB) #necessary for bonds between sidechain and backbone
select new1 or new2
delay 0.025
wireframe 10
select new2
spacefill 4%
select new1 or new2
delay 0.025
wireframe 20
select new2
spacefill 8%
select new1 or new2
delay 0.025
wireframe 30
select new2
spacefill 12%
select new1 or new2
delay 0.025
wireframe 40
select new2
spacefill 16%
select new1 or new2
delay 0.025
wireframe 50
select new2
spacefill 20%
define old *.CA and ~aas
define new1 *.CB and ~aas
define new2 within(2.0,new1) and not old and not new1
select new1 or new2
delay 0.025
wireframe 10
select new2
spacefill 4%
select new1 or new2
delay 0.025
wireframe 20
select new2
spacefill 8%
select new1 or new2
delay 0.025
wireframe 30
select new2
spacefill 12%
select new1 or new2
delay 0.025
wireframe 40
select new2
spacefill 16%
select new1 or new2
delay 0.025
wireframe 50
select new2
spacefill 20%
define old new1
define new1 new2
define new2 within(2.0,new1) and not old and not new1
select new1 or new2
delay 0.025
wireframe 10
select new2
spacefill 4%
select new1 or new2
delay 0.025
wireframe 20
select new2
spacefill 8%
select new1 or new2
delay 0.025
wireframe 30
select new2
spacefill 12%
select new1 or new2
delay 0.025
wireframe 40
select new2
spacefill 16%
select new1 or new2
delay 0.025
wireframe 50
select new2
spacefill 20%
define old new1
define new1 new2
define new2 within(2.0,new1) and not old and not new1
select new1 or new2
delay 0.025
wireframe 10
select new2 and not backbone #makes second connection to backbone for proline but doesn't spacefill the backbone atom
spacefill 4%
select new1 or new2
delay 0.025
wireframe 20
select new2 and not backbone
spacefill 8%
select new1 or new2
delay 0.025
wireframe 30
select new2 and not backbone
spacefill 12%
select new1 or new2
delay 0.025
wireframe 40
select new2 and not backbone
spacefill 16%
select new1 or new2
delay 0.025
wireframe 50
select new2 and not backbone
spacefill 20%
define old new1
define new1 new2
define new2 within(2.0,new1) and not old and not new1 and not backbone #stop extending proline
select new1 or new2
delay 0.025
wireframe 10
select new2
spacefill 4%
select new1 or new2
delay 0.025
wireframe 20
select new2
spacefill 8%
select new1 or new2
delay 0.025
wireframe 30
select new2
spacefill 12%
select new1 or new2
delay 0.025
wireframe 40
select new2
spacefill 16%
select new1 or new2
delay 0.025
wireframe 50
select new2
spacefill 20%
define old new1
define new1 new2
define new2 within(2.0,new1) and not old and not new1 and not backbone
select new1 or new2
delay 0.025
wireframe 10
select new2
spacefill 4%
select new1 or new2
delay 0.025
wireframe 20
select new2
spacefill 8%
select new1 or new2
delay 0.025
wireframe 30
select new2
spacefill 12%
select new1 or new2
delay 0.025
wireframe 40
select new2
spacefill 16%
select new1 or new2
delay 0.025
wireframe 50
select new2
spacefill 20%
# end grow sidechain code
set hermitelevel 4;
connect 3.5 (~target_hbonders) (~nontarget_hbonders) hbond modifyOrCreate
select all
hbonds 0.15
color hbond violet;
" value="show all">
</td>
</tr>
<tr>
<td align="center" colspan="2">
<strong><font face="Verdana, Arial, Helvetica, sans-serif" size="3">Bridged
hydrogen bond using water intermediate:</font></strong><font face="Verdana, Arial, Helvetica, sans-serif" size="3">
</font>
</td>
</tr>
<tr>
<td align="center">
<input name="Submit4" type="submit" script="
script:jmol:1:
exit;
connect (all) (all) hbond delete;
select image all;
remove;
#add image bridgeOne.gif (10,10);
select all;
slab off;
spin off;
halos off;
hbonds off;
labels off;
cartoons on;
color cartoons group;
hbonds off;
select ~core;
spacefill off;
wireframe off;
isosurface off;
delay 1;
moveto 2.0 { -331 -942 50 54.0} 10393.4 0.0 0.0 {13.290001 6.0080004 0.9055} 36.8;
# DEFINE TARGET AND NON-TARGET ATOMS
select atp
define ~target selected
select atomno=3065 or 171:E
define ~non_target selected
# ---------------------------------------------------
# DEFINE TARGET HBONDS WITH WATER
select ~target and (oxygen, nitrogen) and within(3.3, (~non_target and water))
define ~target_to_water selected
select water and within(3.3, ~target and (oxygen, nitrogen))
define ~water_to_target selected
select ~water_to_target or ~target_to_water
define ~all_water_hbonders selected
# ---------------------------------------------------
# DEFINE WATER BRIDGES
# First, define bridging water
select (~non_target and water) and within(3.3, ~target_to_water) and within(3.3, (oxygen, nitrogen) and ~non_target and not water)
define ~bridging_water selected
# Second, define water bridges
select (oxygen, nitrogen) and within(3.3, ~bridging_water) and not water
define ~water_bridges (selected or ~bridging_water)
define ~aas within(group,~water_bridges)
center atomno=1302 or atomno=3065
# ---------------------------------------------------
#-------------------- grow sidechains
set hermitelevel 0
define new1 *.CA and ~aas
define new2 *.CB and ~aas
select (*.CA or *.CB) #necessary for bonds between sidechain and backbone
select new1 or new2
delay 0.025
wireframe 10
select new2
spacefill 4%
select new1 or new2
delay 0.025
wireframe 20
select new2
spacefill 8%
select new1 or new2
delay 0.025
wireframe 30
select new2
spacefill 12%
select new1 or new2
delay 0.025
wireframe 40
select new2
spacefill 16%
select new1 or new2
delay 0.025
wireframe 50
select new2
spacefill 20%
define old *.CA and ~aas
define new1 *.CB and ~aas
define new2 within(2.0,new1) and not old and not new1
select new1 or new2
delay 0.025
wireframe 10
select new2
spacefill 4%
select new1 or new2
delay 0.025
wireframe 20
select new2
spacefill 8%
select new1 or new2
delay 0.025
wireframe 30
select new2
spacefill 12%
select new1 or new2
delay 0.025
wireframe 40
select new2
spacefill 16%
select new1 or new2
delay 0.025
wireframe 50
select new2
spacefill 20%
define old new1
define new1 new2
define new2 within(2.0,new1) and not old and not new1
select new1 or new2
delay 0.025
wireframe 10
select new2
spacefill 4%
select new1 or new2
delay 0.025
wireframe 20
select new2
spacefill 8%
select new1 or new2
delay 0.025
wireframe 30
select new2
spacefill 12%
select new1 or new2
delay 0.025
wireframe 40
select new2
spacefill 16%
select new1 or new2
delay 0.025
wireframe 50
select new2
spacefill 20%
define old new1
define new1 new2
define new2 within(2.0,new1) and not old and not new1
select new1 or new2
delay 0.025
wireframe 10
select new2 and not backbone #makes second connection to backbone for proline but doesn't spacefill the backbone atom
spacefill 4%
select new1 or new2
delay 0.025
wireframe 20
select new2 and not backbone
spacefill 8%
select new1 or new2
delay 0.025
wireframe 30
select new2 and not backbone
spacefill 12%
select new1 or new2
delay 0.025
wireframe 40
select new2 and not backbone
spacefill 16%
select new1 or new2
delay 0.025
wireframe 50
select new2 and not backbone
spacefill 20%
define old new1
define new1 new2
define new2 within(2.0,new1) and not old and not new1 and not backbone #stop extending proline
select new1 or new2
delay 0.025
wireframe 10
select new2
spacefill 4%
select new1 or new2
delay 0.025
wireframe 20
select new2
spacefill 8%
select new1 or new2
delay 0.025
wireframe 30
select new2
spacefill 12%
select new1 or new2
delay 0.025
wireframe 40
select new2
spacefill 16%
select new1 or new2
delay 0.025
wireframe 50
select new2
spacefill 20%
define old new1
define new1 new2
define new2 within(2.0,new1) and not old and not new1 and not backbone
select new1 or new2
delay 0.025
wireframe 10
select new2
spacefill 4%
select new1 or new2
delay 0.025
wireframe 20
select new2
spacefill 8%
select new1 or new2
delay 0.025
wireframe 30
select new2
spacefill 12%
select new1 or new2
delay 0.025
wireframe 40
select new2
spacefill 16%
select new1 or new2
delay 0.025
wireframe 50
select new2
spacefill 20%
# end grow sidechain code
set hermitelevel 4;
connect 3.3 (~water_bridges) (~bridging_water) hbond modifyOrCreate
connect 3.3 (~water_to_target) (~target_to_water) hbond modifyOrCreate
select all
hbonds 0.15
color hbond violet;
" value="1 Example">
</td>
<td align="center">
<input name="Submit11" type="submit" script="
script:jmol:1:
exit;
connect (all) (all) hbond delete;
select image all;
remove;
#add image bridgeAll.gif (10,10);
select all;
slab off;
spin off;
halos off;
hbonds off;
labels off;
cartoons on;
color cartoons group;
hbonds off;
select ~core;
spacefill off;
wireframe off;
isosurface off;
delay 1;
moveto 2 { 15 -994 106 76.4} 1174.8 0.0 0.0 {11.4494295 7.1897593 -0.3249653} 36.2;
# DEFINE TARGET AND NON-TARGET ATOMS
select atp
define ~target selected
select not selected
define ~non_target selected
# ---------------------------------------------------
# DEFINE TARGET HBONDS WITH WATER
select ~target and (oxygen, nitrogen) and within(3.3, (~non_target and water))
define ~target_to_water selected
select water and within(3.3, ~target and (oxygen, nitrogen))
define ~water_to_target selected
select ~water_to_target or ~target_to_water
define ~all_water_hbonders selected
# ---------------------------------------------------
# DEFINE WATER BRIDGES
# First, define bridging water
select (~non_target and water) and within(3.3, ~target_to_water) and within(3.3, (oxygen, nitrogen) and ~non_target and not water)
define ~bridging_water selected
# Second, define water bridges
select (oxygen, nitrogen) and within(3.3, ~bridging_water) and not water
define ~water_bridges (selected or ~bridging_water)
define ~aas within(group,~water_bridges)
center ~all_water_hbonders or ~bridging_water or ~aas
# ---------------------------------------------------
#-------------------- grow sidechains
set hermitelevel 0
define new1 *.CA and ~aas
define new2 *.CB and ~aas
select (*.CA or *.CB) #necessary for bonds between sidechain and backbone
select new1 or new2
delay 0.025
wireframe 10
select new2
spacefill 4%
select new1 or new2
delay 0.025
wireframe 20
select new2
spacefill 8%
select new1 or new2
delay 0.025
wireframe 30
select new2
spacefill 12%
select new1 or new2
delay 0.025
wireframe 40
select new2
spacefill 16%
select new1 or new2
delay 0.025
wireframe 50
select new2
spacefill 20%
define old *.CA and ~aas
define new1 *.CB and ~aas
define new2 within(2.0,new1) and not old and not new1
select new1 or new2
delay 0.025
wireframe 10
select new2
spacefill 4%
select new1 or new2
delay 0.025
wireframe 20
select new2
spacefill 8%
select new1 or new2
delay 0.025
wireframe 30
select new2
spacefill 12%
select new1 or new2
delay 0.025
wireframe 40
select new2
spacefill 16%
select new1 or new2
delay 0.025
wireframe 50
select new2
spacefill 20%
define old new1
define new1 new2
define new2 within(2.0,new1) and not old and not new1
select new1 or new2
delay 0.025
wireframe 10
select new2
spacefill 4%
select new1 or new2
delay 0.025
wireframe 20
select new2
spacefill 8%
select new1 or new2
delay 0.025
wireframe 30
select new2
spacefill 12%
select new1 or new2
delay 0.025
wireframe 40
select new2
spacefill 16%
select new1 or new2
delay 0.025
wireframe 50
select new2
spacefill 20%
define old new1
define new1 new2
define new2 within(2.0,new1) and not old and not new1
select new1 or new2
delay 0.025
wireframe 10
select new2 and not backbone #makes second connection to backbone for proline but doesn't spacefill the backbone atom
spacefill 4%
select new1 or new2
delay 0.025
wireframe 20
select new2 and not backbone
spacefill 8%
select new1 or new2
delay 0.025
wireframe 30
select new2 and not backbone
spacefill 12%
select new1 or new2
delay 0.025
wireframe 40
select new2 and not backbone
spacefill 16%
select new1 or new2
delay 0.025
wireframe 50
select new2 and not backbone
spacefill 20%
define old new1
define new1 new2
define new2 within(2.0,new1) and not old and not new1 and not backbone #stop extending proline
select new1 or new2
delay 0.025
wireframe 10
select new2
spacefill 4%
select new1 or new2
delay 0.025
wireframe 20
select new2
spacefill 8%
select new1 or new2
delay 0.025
wireframe 30
select new2
spacefill 12%
select new1 or new2
delay 0.025
wireframe 40
select new2
spacefill 16%
select new1 or new2
delay 0.025
wireframe 50
select new2
spacefill 20%
define old new1
define new1 new2
define new2 within(2.0,new1) and not old and not new1 and not backbone
select new1 or new2
delay 0.025
wireframe 10
select new2
spacefill 4%
select new1 or new2
delay 0.025
wireframe 20
select new2
spacefill 8%
select new1 or new2
delay 0.025
wireframe 30
select new2
spacefill 12%
select new1 or new2
delay 0.025
wireframe 40
select new2
spacefill 16%
select new1 or new2
delay 0.025
wireframe 50
select new2
spacefill 20%
# end grow sidechain code
set hermitelevel 4;
connect 3.3 (~water_bridges) (~bridging_water) hbond modifyOrCreate
connect 3.3 (~water_to_target) (~target_to_water) hbond modifyOrCreate
select all
hbonds 0.15
color hbond violet;
" value="show all">
</td>
</tr>
<tr>
<td align="center" colspan="2">
<strong><font face="Verdana, Arial, Helvetica, sans-serif" size="3">Polar
interactions with magnesium ions:</font></strong><font face="Verdana, Arial, Helvetica, sans-serif" size="3">
</font>
</td>
</tr>
<tr>
<td align="center">
<input name="Submit5" type="submit" script="
script:jmol:1:
exit;
connect (all) (all) hbond delete;
select image all;
remove;
#add image mgOne.gif (10,10);
select all;
slab off;
spin off;
halos off;
hbonds off;
labels off;
cartoons on;
color cartoons group;
hbonds off;
select ~core;
spacefill off;
wireframe off;
isosurface off;
delay 1;
moveto 2.0 { -457 -888 -60 104.9} 13988.5 0.0 0.0 {14.676 8.154 -3.73} 38.0;
center atomno=2968
define ~aas 184:E
#-------------------- grow sidechains
set hermitelevel 0
define new1 *.CA and ~aas
define new2 *.CB and ~aas
select (*.CA or *.CB) #necessary for bonds between sidechain and backbone
select new1 or new2
delay 0.025
wireframe 10
select new2
spacefill 4%
select new1 or new2
delay 0.025
wireframe 20
select new2
spacefill 8%
select new1 or new2
delay 0.025
wireframe 30
select new2
spacefill 12%
select new1 or new2
delay 0.025
wireframe 40
select new2
spacefill 16%
select new1 or new2
delay 0.025
wireframe 50
select new2
spacefill 20%
define old *.CA and ~aas
define new1 *.CB and ~aas
define new2 within(2.0,new1) and not old and not new1
select new1 or new2
delay 0.025
wireframe 10
select new2
spacefill 4%
select new1 or new2
delay 0.025
wireframe 20
select new2
spacefill 8%
select new1 or new2
delay 0.025
wireframe 30
select new2
spacefill 12%
select new1 or new2
delay 0.025
wireframe 40
select new2
spacefill 16%
select new1 or new2
delay 0.025
wireframe 50
select new2
spacefill 20%
define old new1
define new1 new2
define new2 within(2.0,new1) and not old and not new1
select new1 or new2
delay 0.025
wireframe 10
select new2
spacefill 4%
select new1 or new2
delay 0.025
wireframe 20
select new2
spacefill 8%
select new1 or new2
delay 0.025
wireframe 30
select new2
spacefill 12%
select new1 or new2
delay 0.025
wireframe 40
select new2
spacefill 16%
select new1 or new2
delay 0.025
wireframe 50
select new2
spacefill 20%
define old new1
define new1 new2
define new2 within(2.0,new1) and not old and not new1
select new1 or new2
delay 0.025
wireframe 10
select new2 and not backbone #makes second connection to backbone for proline but doesn't spacefill the backbone atom
spacefill 4%
select new1 or new2
delay 0.025
wireframe 20
select new2 and not backbone
spacefill 8%
select new1 or new2
delay 0.025
wireframe 30
select new2 and not backbone
spacefill 12%
select new1 or new2
delay 0.025
wireframe 40
select new2 and not backbone
spacefill 16%
select new1 or new2
delay 0.025
wireframe 50
select new2 and not backbone
spacefill 20%
define old new1
define new1 new2
define new2 within(2.0,new1) and not old and not new1 and not backbone #stop extending proline
select new1 or new2
delay 0.025
wireframe 10
select new2
spacefill 4%
select new1 or new2
delay 0.025
wireframe 20
select new2
spacefill 8%
select new1 or new2
delay 0.025
wireframe 30
select new2
spacefill 12%
select new1 or new2
delay 0.025
wireframe 40
select new2
spacefill 16%
select new1 or new2
delay 0.025
wireframe 50
select new2
spacefill 20%
define old new1
define new1 new2
define new2 within(2.0,new1) and not old and not new1 and not backbone
select new1 or new2
delay 0.025
wireframe 10
select new2
spacefill 4%
select new1 or new2
delay 0.025
wireframe 20
select new2
spacefill 8%
select new1 or new2
delay 0.025
wireframe 30
select new2
spacefill 12%
select new1 or new2
delay 0.025
wireframe 40
select new2
spacefill 16%
select new1 or new2
delay 0.025
wireframe 50
select new2
spacefill 20%
# end grow sidechain code
set hermitelevel 4;
connect 3.3 (atomno=2968) (all) hbond modifyOrCreate
select all
hbonds 0.15
color hbond violet;
" value="1 Example">
</td>
<td align="center">
<input name="Submit12" type="submit" script="
script:jmol:1:
exit;
connect (all) (all) hbond delete;
select image all;
remove;
#add image mgOne.gif (10,10);
select all;
slab off;
spin off;
halos off;
hbonds off;
labels off;
cartoons on;
color cartoons group;
hbonds off;
select ~core;
spacefill off;
wireframe off;
isosurface off;
delay 1;
moveto 2.0 { -539 -825 171 56.5} 10337.5 0.0 0.0 {14.1154995 7.5285 -1.9305} 36.9;
center atomno=2968 or atomno=2969
define ~aas within(group, within(3.3,mn))
#-------------------- grow sidechains
set hermitelevel 0
define new1 *.CA and ~aas
define new2 *.CB and ~aas
select (*.CA or *.CB) #necessary for bonds between sidechain and backbone
select new1 or new2
delay 0.025
wireframe 10
select new2
spacefill 4%
select new1 or new2
delay 0.025
wireframe 20
select new2
spacefill 8%
select new1 or new2
delay 0.025
wireframe 30
select new2
spacefill 12%
select new1 or new2
delay 0.025
wireframe 40
select new2
spacefill 16%
select new1 or new2
delay 0.025
wireframe 50
select new2
spacefill 20%
define old *.CA and ~aas
define new1 *.CB and ~aas
define new2 within(2.0,new1) and not old and not new1
select new1 or new2
delay 0.025
wireframe 10
select new2
spacefill 4%
select new1 or new2
delay 0.025
wireframe 20
select new2
spacefill 8%
select new1 or new2
delay 0.025
wireframe 30
select new2
spacefill 12%
select new1 or new2
delay 0.025
wireframe 40
select new2
spacefill 16%
select new1 or new2
delay 0.025
wireframe 50
select new2
spacefill 20%
define old new1
define new1 new2
define new2 within(2.0,new1) and not old and not new1
select new1 or new2
delay 0.025
wireframe 10
select new2
spacefill 4%
select new1 or new2
delay 0.025
wireframe 20
select new2
spacefill 8%
select new1 or new2
delay 0.025
wireframe 30
select new2
spacefill 12%
select new1 or new2
delay 0.025
wireframe 40
select new2
spacefill 16%
select new1 or new2
delay 0.025
wireframe 50
select new2
spacefill 20%
define old new1
define new1 new2
define new2 within(2.0,new1) and not old and not new1
select new1 or new2
delay 0.025
wireframe 10
select new2 and not backbone #makes second connection to backbone for proline but doesn't spacefill the backbone atom
spacefill 4%
select new1 or new2
delay 0.025
wireframe 20
select new2 and not backbone
spacefill 8%
select new1 or new2
delay 0.025
wireframe 30
select new2 and not backbone
spacefill 12%
select new1 or new2
delay 0.025
wireframe 40
select new2 and not backbone
spacefill 16%
select new1 or new2
delay 0.025
wireframe 50
select new2 and not backbone
spacefill 20%
define old new1
define new1 new2
define new2 within(2.0,new1) and not old and not new1 and not backbone #stop extending proline
select new1 or new2
delay 0.025
wireframe 10
select new2
spacefill 4%
select new1 or new2
delay 0.025
wireframe 20
select new2
spacefill 8%
select new1 or new2
delay 0.025
wireframe 30
select new2
spacefill 12%
select new1 or new2
delay 0.025
wireframe 40
select new2
spacefill 16%
select new1 or new2
delay 0.025
wireframe 50
select new2
spacefill 20%
define old new1
define new1 new2
define new2 within(2.0,new1) and not old and not new1 and not backbone
select new1 or new2
delay 0.025
wireframe 10
select new2
spacefill 4%
select new1 or new2
delay 0.025
wireframe 20
select new2
spacefill 8%
select new1 or new2
delay 0.025
wireframe 30
select new2
spacefill 12%
select new1 or new2
delay 0.025
wireframe 40
select new2
spacefill 16%
select new1 or new2
delay 0.025
wireframe 50
select new2
spacefill 20%
# end grow sidechain code
set hermitelevel 4;
connect 3.3 (mn) (all) hbond modifyOrCreate
select all
hbonds 0.15
color hbond violet;
" value="show all">
</td>
</tr>
<tr>
<td align="center" colspan="2">
<strong><font face="Verdana, Arial, Helvetica, sans-serif" size="3">View
all types of interactions:</font></strong><font face="Verdana, Arial, Helvetica, sans-serif" size="3">
</font>
</td>
</tr>
<tr>
<td align="center" colspan="2">
<input name="Submit13" type="submit" script="
script:jmol:1:
exit;
connect (all) (all) hbond delete;
select image all;
remove;
#add image allAll.gif (10,10);
select all;
slab off;
spin off;
halos off;
hbonds off;
labels off;
cartoons on;
color cartoons group;
hbonds off;
select ~core;
spacefill off;
wireframe off;
isosurface off;
delay 1;
moveto 2 { 404 881 244 23.7} 786.9 0.0 0.0 {9.00922 9.745092 2.718593} 39.2;
define ~aas within(group,within(4.5,atp)) or within(group,within(4.5,(within(3.3,atp) and water)))
#---------- define hydrophobic
select atp
define ~target selected
select not selected and not solvent
define ~non_target selected
select (~non_target and (carbon,sulfur,selenium) and within(4.5, (~target and (carbon,sulfur,selenium))))
define ~nontarget_phobic selected
select (~target and (carbon,sulfur,selenium) and within(4.5, (~non_target and (carbon,sulfur,selenium))))
define ~target_phobic selected
select ~target_phobic or ~nontarget_phobic
define ~all_phobic selected
#---------- define direct hbonds
select atp
define ~target selected
select not selected and not solvent
define ~non_target selected
select (~non_target and (oxygen, nitrogen) and within(3.5, (~target and (oxygen, nitrogen))))
define ~nontarget_hbonders selected
select (~target and (oxygen, nitrogen) and within(3.5, (~non_target and (oxygen, nitrogen))))
define ~target_hbonders selected
select ~target_hbonders or ~nontarget_hbonders
define ~all_hbonders selected
#----------- define bridged
select atp
define ~target selected
select not selected
define ~non_target selected
select ~target and (oxygen, nitrogen) and within(3.3, (~non_target and water))
define ~target_to_water selected
select water and within(3.3, ~target and (oxygen, nitrogen))
define ~water_to_target selected
select ~water_to_target or ~target_to_water
define ~all_water_hbonders selected
select (~non_target and water) and within(3.3, ~target_to_water) and within(3.3, (oxygen, nitrogen) and ~non_target and not water)
define ~bridging_water selected
select (oxygen, nitrogen) and within(3.3, ~bridging_water) and not water
define ~water_bridges (selected or ~bridging_water)
#-------------------- grow sidechains
set hermitelevel 0
define new1 *.CA and ~aas
define new2 *.CB and ~aas
select (*.CA or *.CB) #necessary for bonds between sidechain and backbone
select new1 or new2
delay 0.025
wireframe 10
select new2
spacefill 4%
select new1 or new2
delay 0.025
wireframe 20
select new2
spacefill 8%
select new1 or new2
delay 0.025
wireframe 30
select new2
spacefill 12%
select new1 or new2
delay 0.025
wireframe 40
select new2
spacefill 16%
select new1 or new2
delay 0.025
wireframe 50
select new2
spacefill 20%
define old *.CA and ~aas
define new1 *.CB and ~aas
define new2 within(2.0,new1) and not old and not new1
select new1 or new2
delay 0.025
wireframe 10
select new2
spacefill 4%
select new1 or new2
delay 0.025
wireframe 20
select new2
spacefill 8%
select new1 or new2
delay 0.025
wireframe 30
select new2
spacefill 12%
select new1 or new2
delay 0.025
wireframe 40
select new2
spacefill 16%
select new1 or new2
delay 0.025
wireframe 50
select new2
spacefill 20%
define old new1
define new1 new2
define new2 within(2.0,new1) and not old and not new1
select new1 or new2
delay 0.025
wireframe 10
select new2
spacefill 4%
select new1 or new2
delay 0.025
wireframe 20
select new2
spacefill 8%
select new1 or new2
delay 0.025
wireframe 30
select new2
spacefill 12%
select new1 or new2
delay 0.025
wireframe 40
select new2
spacefill 16%
select new1 or new2
delay 0.025
wireframe 50
select new2
spacefill 20%
define old new1
define new1 new2
define new2 within(2.0,new1) and not old and not new1
select new1 or new2
delay 0.025
wireframe 10
select new2 and not backbone #makes second connection to backbone for proline but doesn't spacefill the backbone atom
spacefill 4%
select new1 or new2
delay 0.025
wireframe 20
select new2 and not backbone
spacefill 8%
select new1 or new2
delay 0.025
wireframe 30
select new2 and not backbone
spacefill 12%
select new1 or new2
delay 0.025
wireframe 40
select new2 and not backbone
spacefill 16%
select new1 or new2
delay 0.025
wireframe 50
select new2 and not backbone
spacefill 20%
define old new1
define new1 new2
define new2 within(2.0,new1) and not old and not new1 and not backbone #stop extending proline
select new1 or new2
delay 0.025
wireframe 10
select new2
spacefill 4%
select new1 or new2
delay 0.025
wireframe 20
select new2
spacefill 8%
select new1 or new2
delay 0.025
wireframe 30
select new2
spacefill 12%
select new1 or new2
delay 0.025
wireframe 40
select new2
spacefill 16%
select new1 or new2
delay 0.025
wireframe 50
select new2
spacefill 20%
define old new1
define new1 new2
define new2 within(2.0,new1) and not old and not new1 and not backbone
select new1 or new2
delay 0.025
wireframe 10
select new2
spacefill 4%
select new1 or new2
delay 0.025
wireframe 20
select new2
spacefill 8%
select new1 or new2
delay 0.025
wireframe 30
select new2
spacefill 12%
select new1 or new2
delay 0.025
wireframe 40
select new2
spacefill 16%
select new1 or new2
delay 0.025
wireframe 50
select new2
spacefill 20%
# end grow sidechain code
set hermitelevel 4;
connect 4.5 (~target_phobic) (~nontarget_phobic) hbond modifyOrCreate
select (~target_phobic) or (~nontarget_phobic)
hbonds 0.1
color hbond lightgreen;
connect 3.5 (~target_hbonders) (~nontarget_hbonders) hbond modifyOrCreate
select (~target_hbonders) or (~nontarget_hbonders)
hbonds 0.15
color hbond violet;
connect 3.3 (~water_bridges) (~bridging_water) hbond modifyOrCreate
select (~water_bridges) or (~bridging_water)
hbonds 0.15
color hbond violet;
connect 3.3 (~water_to_target) (~target_to_water) hbond modifyOrCreate
select (~water_to_target) or (~target_to_water)
hbonds 0.15
color hbond violet;
connect 3.3 (mn) (all) hbond modifyOrCreate
select (mn) or within(3.3,mn)
hbonds 0.15
color hbond violet;
" value="show all">
</td>
</tr>
</table>
</form>
</body>
</html>
-4a214b
Raised Bevel
18true
8.0
1
org.concord.modeler.text.LineIcon0.751false-10000000 26 70
1
0 26 708
1
2 0 24
upBackSmall.gifdrugPage5.cml
upContents.gifdrugIndex.cml
1
0 26 70
0 26 70