Mucin1 is an important tumor marker, and is notable for the autoproteolytic event, a signature of all SEA domain containing proteins. This work reports an in silico, study of the structural and functional significance of the 18 residue insert in the autoproteolytic process and also the peptide inhibitors for preventing its receptor-ligand alliance. It also reports ligand scaffolds that could effectively participate in inhibition of autoproteolysis of mucin 1. The study reveals both isoforms to poses an intact SEA domain, with an altered functional scaffold around the cleavage site. Mutation analysis by alanine substitutions at the insert region revealed ILE67 to be more destabilizing, resulting in increased fluctuation of the neighboring residues. Furthermore, molecular dynamics simulation revealed Isoleucine67 to contribute more to the structural and functional properties of the protein and therefore is one of the crucial residues for the cleavable nature of MUC1/X. Through virtual screeing and docking two ligand scaffolds were identified that have higher binding affinity towards the cleavage site.