Sandbox 35: Difference between revisions
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====Ligands interactions and Pseudo Substrates==== | ====Ligands interactions and Pseudo Substrates==== | ||
Papain is said to have 29 methanol molecules that encircle around it as <scene name='Sandbox_35/Papain_ligand/1'>ligands</scene>. The polarity of the ligands | Papain is said to have 29 methanol molecules that encircle around it as <scene name='Sandbox_35/Papain_ligand/1'>ligands</scene>. The polarity of the ligands result in hydrogen bonding interactions, possibly providing further stability for papain structure. <ref>PMID: 6502713</ref> | ||
<scene name='Sandbox_35/Cathepsin_l_specific_inhibitor/3'>Cathepsin L specific inhibitor</scene> is part of a series of CLIK . < | <scene name='Sandbox_35/Cathepsin_l_specific_inhibitor/3'>Cathepsin L specific inhibitor</scene> is part of a series known as CLIK inhibitors and was used on Papain for assessment of specificity in inhibition. The difference in structure between Papain-CLIK 148 complex and orginial papain is not very drastic. The changes result primarily from alterations in surface proteins except on Cys 25 where a covalent bond is formed with the C2 on CLIK 148. The primarily <scene name='Sandbox_35/Cathepsin_interaction/3'>interactions</scene> between pseudo substrate/inhibitor and papain were non-water hydrogen bonds and mostly hydrophobic interactions. CLIK 148's binding to the active site of papain is in a non-substrate mode with the main site showing pyrimidine ring interaction between Trp 177 and CLIK 148. Hydrogen bonding is observed between the oxygens in CLIK 148 to Gln 19 and Gly 66. Moreover, a water molecule has been observed to be near the His 159 residue enabling greater hydrogen bonding, once again highlighting solvents role in stability. <ref>PMID: 10600517</ref> | ||
