Sometimes you do not have to create your prospective lead molecule (first ligand molecule to start). In our example, one of the ligand molecules is already in the PDB molecule. It was crystalized while safinamide molecule and we can get it from PDB file.
In the beginning, the strategy of the experiment could be seen a little odd. We are getting a ligand structure form an already docked complex and trying to dock again into the same target! The result should be obvious, right? Yes, that is correct but while we are searching for a new molecule the known lead molecule will help us to find novel therapeutics. Actually, that is why we call it lead molecule.
We will separate the safinamide from MAO-B and re-dock them with a docking tool. While doing that we will be sure about our experiment process. After that make small changes to the lead molecule and invent brand new ligands. After that, the testing (the docking) process will come in handy.
When I review the downloaded target molecule I can see the extra section of atoms. This part is generally indicated with HTATM type. But be careful. FAD is also indicated similarly and it is part of MAO-B. Is it even the binding part of MAO-B. At this point, you have to have some general idea about this target molecule. You can find the reference article which is authored by the scientists who make the crystallography.
Get the safinamide part and save it as ligand.pdb. In the next sections we will concert it into PDBQT format.
NEXT: Converting the target molecule into PDBQT.