Sandbox 80: Difference between revisions
No edit summary |
No edit summary |
||
| Line 3: | Line 3: | ||
This is an antiviral drug used to treat HIV by inhibiting proteases in the virus. This inhibition causes the spread of the virus to decrease significantly. The <scene name='Sandbox_80/Protease/1'>protease</scene> is an enzyme that the virus uses to produce the proteins necessary to assemble more viruses. | This is an antiviral drug used to treat HIV by inhibiting proteases in the virus. This inhibition causes the spread of the virus to decrease significantly. The <scene name='Sandbox_80/Protease/1'>protease</scene> is an enzyme that the virus uses to produce the proteins necessary to assemble more viruses. | ||
The common name for saqinavir is fortovase. It functions as peptide-like analogue that binds to <scene name='Sandbox_80/Ac_1/1'>active site 1</scene> of the protein and causes inhibition by preventing the protease from cleaving polyproteins which in turn causes the virus to create non-infectious virus particles. | The common name for saqinavir is fortovase. It functions as peptide-like analogue that binds to <scene name='Sandbox_80/Ac_1/1'>active site 1</scene> of the protein and causes inhibition by preventing the protease from cleaving polyproteins which in turn causes the virus to create non-infectious virus particles. This drug is often used in combination with other HIV medications to produce a more potent effect. | ||
| Line 14: | Line 14: | ||
==Protein and Drug interations== | ==Protein and Drug interations== | ||
intermolecular forces that cause the drug to bind in the active site of the protease are prodominantly H-bonds to | intermolecular forces that cause the drug to bind in the active site of the protease are prodominantly H-bonds to | ||
<scene name='Sandbox_80/Hydrophilic/1'>hydrophilic groups</scene> | <scene name='Sandbox_80/Hydrophilic/1'>hydrophilic groups</scene>. The carboxylic acid group in the <scene name='Sandbox_80/Asp_25/1'>Aspartic Acid</scene> residue 25 binds with the hydroxyl group of Saquinavir. | ||
==References== | ==References== | ||
http://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0000973 | http://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0000973 | ||
http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=60934&loc=ec_rcs#pharmaction | http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=60934&loc=ec_rcs#pharmaction | ||
Latest revision as of 16:29, 11 March 2011
Template:Tims Sandbox Reservation
This is an antiviral drug used to treat HIV by inhibiting proteases in the virus. This inhibition causes the spread of the virus to decrease significantly. The protease is an enzyme that the virus uses to produce the proteins necessary to assemble more viruses. The common name for saqinavir is fortovase. It functions as peptide-like analogue that binds to active site 1 of the protein and causes inhibition by preventing the protease from cleaving polyproteins which in turn causes the virus to create non-infectious virus particles. This drug is often used in combination with other HIV medications to produce a more potent effect.
| |||||||||||||
| 3oxc, resolution 1.16Å (default scene) | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Ligands: | FMT, ROC, SO4 | ||||||||||||
| Gene: | pol (Human immunodeficiency virus 1) | ||||||||||||
| Activity: | HIV-1 retropepsin, with EC number 3.4.23.16 | ||||||||||||
| Related: | 2ien, 3mws, 3nu3, 3cyx, 3d1x, 3d1y, 2nmy, 2nmz, 2nnk, 2nnp | ||||||||||||
| |||||||||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||||||||
Structure
The chemical formula of Saquinavir is (C39)(H54)(N6)(O8)S and the molecular weight is 766.94 g/mol.There are 5 aromatic rings, two of which are heterocyclic. One hydroxyl group near the center of the compound that plays an important role in active site binding. The amino groups cause the protease to recognize the drug as a natural substrate with amino acid groups which are recognized by the active sites.
Protein and Drug interations
intermolecular forces that cause the drug to bind in the active site of the protease are prodominantly H-bonds to hydrophilic groups. The carboxylic acid group in the Aspartic Acid residue 25 binds with the hydroxyl group of Saquinavir.
References
https://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0000973 https://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=60934&loc=ec_rcs#pharmaction
