In order to understand the mechanism of molecular interactions at active sites of trafficking protein particle complex (TRAPPC) subunit 3-like protein (Accession number Q5T215) homology modeling and docking studies were taken up. We generated a three-dimensional (3D) model of target protein based on the Crystal structure of Human BET3 protein (PDB code 1SZ7) using modeller software. Under the process of homology modeling 25 models were generated, and the model having the lowest modeler objective function value was chosen for further assessment. The generated model was assessed and validated using PROCHECK software and found to be reliable.With the generated model, we carried out a flexible docking study using the FlexX docking tool available on the Sybyl Software in order to find better antagonist site for drug binding. We carried out a flexible docking with the Palmatic acid and Donepezil as ligands; these were found to bind at LEU87, LYS84 and THR90 residues on given generated protein in our studies. We therefore concluded that the above mentioned residues were the key residue sites for ligand binding showing strong hydrogen bonding contacts.The target protein is more prevalently seen in the amygdala region of brain which forms one of the key subunit of TRAPP complex. As per functional similarity with BET3, target protein might play key role in trafficking abnormally folded A-beta and tau proteins along endoplasmic reticulum to Golgi apparatus there by leading to formation of senile plaques in various regions of brain, whose accumulation causes Alzheimer’s disease.