The structural investigation of the ligand/target interactions represents a challenging task in the field of drug discovery or lead compound optimization. In the present study, a computational approach allowed the identification of the binding site of A9 peptide, within a synthetic model of HER2 receptor (HER2-DIVMP). To this aim, molecular docking calculations and molecular dynamics simulations were employed, taking into account experimental data obtained by fluorescence studies. The computational model was further validated by performing fluorescence binding studies between the ligand A9 and HER2-DIVMP mutants, prepared by replacing key amino acid residues. A new binding pocket of HER2-DIVMP was identified, which could be fruitfully exploited for future lead-optimization studies.