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 PyRx<ref>Small-Molecule Library Screening by Docking with PyRx. Dallakyan S, Olson AJ. Methods Mol Biol. 2015;1263:243-50.</ref> to actually bind dCMP to 3HDT. Then PyMOL was used to visualize the binding pockets and dCMP 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. However, this area was where dCMP binded 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 in the protein with hydrophobic interactions. Also, there are two residues, <scene name='90/904996/Dcmp_with_3hdt_active_site/1'>Lys146 (yellow) and Leu 202 (purple)</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 because during the docking process on PyRx, we were unsuccessful in getting the program to recognize where the ATP was bound in the protein first before docking our substrate with ATP already in the protein.