Sandbox Reserved 425: Difference between revisions

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===Binding Interactions===

Met 40, Leu 198, and Tyr 200 define the pocket for the 4-phenyl-7, 8-dihydroxycoumarine (4PCM) ligand binding site. Trp 38 and Pro 174 make Van der Waals interactions with the 4PCM. The magnesium ion interacts with the two hydroxyl groups of the 4PCM. The magnesium ion also aids in the protonation of Lys 144, causing an electrostatic interaction with a hydroxyl group of 4PCM. The other end of this Lys 144 then acts a hydrogen bond donor for a water molecule in the binding pocket. This water molecule then acts a hydrogen bond donor for the carbonyl group of 4PCM, creating an interesting network of hydrogen bonds. The above interactions stabilize the ligand in the binding pocket. These interactions are somewhat similar to other inhibitors previously used, however some differences do occur that make past inhibitors more stable. In our 4PCM, we can see a bond angle between the sulfur and carbon atoms of <scene name='Sandbox_Reserved_425/Met_40/1'>Met 40</scene> to be significantly less than that of the Met 40 in a COMT complex using <scene name='Sandbox_Reserved_425/3_5-dinitrocatchetol/1'>3,5-dinitrocatchetol</scene> as an inhibitor instead; the change is about 96o.

Met 40, Leu 198, and Tyr 200 define the scene name='Sandbox_Reserved_425/Pocket/1'>pocket</scene> for the 4-phenyl-7, 8-dihydroxycoumarine (4PCM) ligand binding site. Trp 38 and Pro 174 make Van der Waals interactions with the 4PCM. The magnesium ion interacts with the two hydroxyl groups of the 4PCM. The magnesium ion also aids in the protonation of Lys 144, causing an electrostatic interaction with a hydroxyl group of 4PCM. The other end of this Lys 144 then acts a hydrogen bond donor for a water molecule in the binding pocket. This water molecule then acts a hydrogen bond donor for the carbonyl group of 4PCM, creating an interesting network of hydrogen bonds. The above interactions stabilize the ligand in the binding pocket. These interactions are somewhat similar to other inhibitors previously used, however some differences do occur that make past inhibitors more stable. In our 4PCM, we can see a bond angle between the sulfur and carbon atoms of <scene name='Sandbox_Reserved_425/Met_40/1'>Met 40</scene> to be significantly less than that of the Met 40 in a COMT complex using <scene name='Sandbox_Reserved_425/3_5-dinitrocatchetol/1'>3,5-dinitrocatchetol</scene> as an inhibitor instead; the change is about 96o.

Sandbox Reserved 425: Difference between revisions

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 ===Binding Interactions===
 <Structure load='2zvj' size='500' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' />
-Met 40, Leu 198, and Tyr 200 define the pocket for the 4-phenyl-7, 8-dihydroxycoumarine (4PCM) ligand binding site. Trp 38 and Pro 174 make Van der Waals interactions with the 4PCM. The magnesium ion interacts with the two hydroxyl groups of the 4PCM. The magnesium ion also aids in the protonation of Lys 144, causing an electrostatic interaction with a hydroxyl group of 4PCM. The other end of this Lys 144 then acts a hydrogen bond donor for a water molecule in the binding pocket. This water molecule then acts a hydrogen bond donor for the carbonyl group of 4PCM, creating an interesting network of hydrogen bonds. The above interactions stabilize the ligand in the binding pocket. These interactions are somewhat similar to other inhibitors previously used, however some differences do occur that make past inhibitors more stable. In our 4PCM, we can see a bond angle between the sulfur and carbon atoms of <scene name='Sandbox_Reserved_425/Met_40/1'>Met 40</scene> to be significantly less than that of the Met 40 in a COMT complex using <scene name='Sandbox_Reserved_425/3_5-dinitrocatchetol/1'>3,5-dinitrocatchetol</scene> as an inhibitor instead; the change is about 96o.
+Met 40, Leu 198, and Tyr 200 define the scene name='Sandbox_Reserved_425/Pocket/1'>pocket</scene> for the 4-phenyl-7, 8-dihydroxycoumarine (4PCM) ligand binding site. Trp 38 and Pro 174 make Van der Waals interactions with the 4PCM. The magnesium ion interacts with the two hydroxyl groups of the 4PCM. The magnesium ion also aids in the protonation of Lys 144, causing an electrostatic interaction with a hydroxyl group of 4PCM. The other end of this Lys 144 then acts a hydrogen bond donor for a water molecule in the binding pocket. This water molecule then acts a hydrogen bond donor for the carbonyl group of 4PCM, creating an interesting network of hydrogen bonds. The above interactions stabilize the ligand in the binding pocket. These interactions are somewhat similar to other inhibitors previously used, however some differences do occur that make past inhibitors more stable. In our 4PCM, we can see a bond angle between the sulfur and carbon atoms of <scene name='Sandbox_Reserved_425/Met_40/1'>Met 40</scene> to be significantly less than that of the Met 40 in a COMT complex using <scene name='Sandbox_Reserved_425/3_5-dinitrocatchetol/1'>3,5-dinitrocatchetol</scene> as an inhibitor instead; the change is about 96o.