Sandbox Reserved 428: Difference between revisions

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<scene name='48/483885/Protein_with_inhibitor/3'> Binding of the SAM inhibitor </scene> does not change the structure of the protein to a great degree, the RMS difference of the Cα atoms is 0.49 angstroms.

The relatively <scene name='48/483885/3p8z_binding/3'>hydrophilic SAM ligand binds into the deep pocket</scene>. Favorable hydrogen bonds are satisfied in this interaction along with hydrophobic interactions between the non-polar residues and the non-polar portions of the inhibitor. The bonds are satisfied with the following amino acids on the protein, Phe-133, Ile-147, Gly-148, Glu-149, Arg-160, Arg-163, Val-164, and Leu-182. These residues help to stabilize the charges present on the ligand; they are not all strictly hydrophilic, however they do have portions that allow for hydrogen bonding.

The relatively <scene name='48/483885/3p8z_binding/3'>hydrophilic SAM ligand binds into the deep pocket</scene>. Favorable hydrogen bonds are satisfied in this interaction along with hydrophobic interactions between the non-polar residues and the non-polar portions of the inhibitor. The bonds are satisfied with the following amino acids on the protein, Phe-133, Ile-147, Gly-148, Glu-149, Arg-160, Arg-163, Val-164, and Leu-182. These residues help to stabilize the charges present on the ligand; they are not all strictly hydrophilic, however they do have portions that allow for hydrogen bonding.<ref>http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3057852/</ref>

Competitive binding on this active site could prove to be an effective drug target; if the SAM ligand cannot bind then the viral RNA cap will not be methylated. This could lead to a less viable virus due to a incorrectly formed 5' cap on the viral RNA.

Sandbox Reserved 428: Difference between revisions

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@@ Line 31: / Line 31: @@
 <scene name='48/483885/Protein_with_inhibitor/3'> Binding of the SAM inhibitor </scene> does not change the structure of the protein to a great degree, the RMS difference of the Cα atoms is 0.49 angstroms.
-The relatively <scene name='48/483885/3p8z_binding/3'>hydrophilic SAM ligand binds into the deep pocket</scene>.  Favorable hydrogen bonds are satisfied in this interaction along with hydrophobic interactions between the non-polar residues and the non-polar portions of the inhibitor.  The bonds are satisfied with the following amino acids on the protein, Phe-133, Ile-147, Gly-148, Glu-149, Arg-160, Arg-163, Val-164, and Leu-182.  These residues help to stabilize the charges present on the ligand; they are not all strictly hydrophilic, however they do have portions that allow for hydrogen bonding.
+The relatively <scene name='48/483885/3p8z_binding/3'>hydrophilic SAM ligand binds into the deep pocket</scene>.  Favorable hydrogen bonds are satisfied in this interaction along with hydrophobic interactions between the non-polar residues and the non-polar portions of the inhibitor.  The bonds are satisfied with the following amino acids on the protein, Phe-133, Ile-147, Gly-148, Glu-149, Arg-160, Arg-163, Val-164, and Leu-182.  These residues help to stabilize the charges present on the ligand; they are not all strictly hydrophilic, however they do have portions that allow for hydrogen bonding.<ref>http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3057852/</ref>
 Competitive binding on this active site could prove to be an effective drug target; if the SAM ligand cannot bind then the viral RNA cap will not be methylated.  This could lead to a less viable virus due to a incorrectly formed 5' cap on the viral RNA.