Human Histone deacetylase and vorinostat (4LXZ)

sketchfab

I began by tracking down the pdb file associated with the protein-drug complex, as well as relevant journal articles to serve as context. Next, I loaded the pdb file into Pymol and performed some initial cleanup on the model. Following that, I delved into research on the intricate relationships between proteins and drugs within this system. My investigation led me to identify five key interactions: hydrogen bonding, ion chelation, leucine rotamers, hydrophobic interactions, and polar interactions. Notably, the off-rotamer of leucine proved to be a relatively weak interaction with vorinostat, yet its mechanism piqued my interest, prompting me to retain it in my analysis. I then pinpointed all residues relevant to these protein-drug interactions and customized their animation, coloring, and surface interactions. Subsequently, I crafted a concise description of the protein-drug interactions and imported my Pymol file into Sketchfab. After fine-tuning the background settings, I positioned the camera angles to optimize annotations for protein-drug interaction details before replicating the information from my notes.