Hormone-related mammary gland tumors are among the most commonly diagnosed neoplasms in female dogs. Estrogen enacts its biological roles through specific receptors known as estrogen receptors (ER). In human medicine, anti-estrogen therapy has become the gold standard in ER-positive breast tumors' therapeutic regimen. The binding pocket of the canine estrogen receptor alpha (cERα) ligand binding domain comprises of three key amino acid residues including E354, G522 and L526, which stabilize the cERα-E2 interaction via hydrogen bonding. The side chain of E354 shares hydrogen bond interaction with the A ring of its natural ligand E2, whereas the main chain of G522 and L526 interact with the E2-D ring. The single mutation of the E354 aberrant, along with the hydrogen bond interaction between cERα and both ligands, leads to a variety of binding affinities. According to this in silico model, it may be concluded that E354 plays a role in the cERα activities. The effects of single mutants might need to be studied further in vitro and in vivo.