Internationally about one billion people are estimated to be iodine deficient; however, it is unknown how often this results in hypothyroidism. In this present research investigation, we focus on the potential motif sequence for the mutated gene coded protein related to hypothyrodism disorder. The FOXE1 peptide sequence modeling is based on the Helix-Turn-Helix (HTH) motif sequence. We used advanced peptide modeling server for methodology studies. The final results of our project clearly explain that the identified motif –peptide sequence and the 3D peptide structure are potential candidates for drug docking studies and also act as novel molecular markers useful for pharmacoinformitics and clinical endocrinology studies.