BASIL2022GV3HDT: Difference between revisions

We used POCASA <ref>J. Yu, Y. Zhou, I. Tanaka, M. Yao, Roll: A new algorithm for the detection of protein pockets and cavities with a rolling probe sphere. Bioinformatics, 26(1), 46-52, (2010) [PMID: 19846440]</ref> to determine potential binding pockets within our protein, and then PyRx<ref>Small-Molecule Library Screening by Docking with PyRx. Dallakyan S, Olson AJ. Methods Mol Biol. 2015;1263:243-50.</ref> to dock dCMP into 3HDT. PyMOL<ref>The PyMOL Molecular Graphics System, Version 1.7.4.5 Edu Schrödinger, LLC.</ref> was then used to visualize the binding pockets and dCMP docked in the protein. This <scene name='90/904996/Binding_pockets/1'>binding pocket</scene> (in purple) is a potential pocket the substrate dCMP may bind to in the protein, 3HDT. This area was also where dCMP bound with the highest affinity in PyRx. The <scene name='90/904996/Hydrophobic_interactions/1'>amino acids</scene> (Gly21, Ser22, Gly23, Val27, Thr 142, Gln149, Arg150, Thr197, Leu200, Thr201) interact within that area to help hold the substrate in place with hydrophobic interactions. Also, there are two residues, <scene name='90/904996/Dcmp_with_3hdt_active_site/1'>Lys146 (purple) and Leu 202 (yellow)</scene> within the active site containing dCMP and cofactor ATP that are important in substrate binding. They interact with the substrate forming hydrogen bonds with the oxygens on the phosphate groups and the 6-membered ring. However, these results may not be as accurate due to an issue in the docking process where we were unsuccessful in getting PyRx to recognize where the ATP cofactor was bound before docking our substrate into the protein.