Peroxisome proliferator-activated receptors (PPARs) is composed of three receptors as a group (PPARα, PPARγ, and PPARδ). Activation of the PPARs with a pan-agonist is used for the clinical treatment of Type-2 diabetes mellitus (T2DM). We use the FMOPhore algorithm to scan the binding site of the apo-structure of the PPAR, classify hotspots and develop a 3D-pharmacophore model for development of active molecules.