The 6.12 kDa human epidermal growth factor (hEGF) protein is expressed in the body and plays a role in cell proliferation and differentiation. This research aims to isolate the hEGF genes, determine the phylogenetic relationship between organisms based on the hEGF gene, construct the 3D structure of the hEGF protein, and identify the precise binding position between the hEGF protein and the tested Myosin-9. DNA was isolated from blood of healthy individuals followed by amplification using specified primers. DNA sequencing was utilized to identify the amplification results before generating the  phylogenetic trees. The retrieved sequences were then modeled using the Swiss model and docking proteins in silico. In three samples, DNA was successfully amplified to 700 bp and the phylogenetic analysis revealed that the three hEGF gene samples belonged to the same clades. With a 30 % identity seq, aligned result sequences modeled using the Swiss model created proteins which were not homologous. The outcomes of this modeling were compared to the hEGF protein from the database, which had a sequence identity of greater than 90 %. The i-RMSD value of the target protein (5.4 +/- 0.4), the Van der Waals energy (-29.3 +/- 1.7), and the Z-score were determined by simulation (-1.7). These results indicate a potential interaction between the isolated EGF protein and the myosin-9 tested. HIGHLIGHTS Human Epidermal Growth Factor (hEGF) protein is a potential protein expressed in the body and plays a role in cell proliferation and differentiation Isolation of the EGF gene through human blood can be carried out to get data on protein size, phylogenetic analysis, and protein structure The results of in vitro study were modeled in silico to obtain the three-dimensional structure as well as intermolecular interactions of the protein Information beginning this study is used in follow-up research to predict EGF communications with other molecules GRAPHICAL ABSTRACT