Noggin (NOG) a BMP (bone morphogenetic protein) antagonist plays a key role in preferentially driving a subset of breast cancer cells towards the bone and causing osteolytic lesions leading to severe pain and discomfort in the patients. Owing to its role in bone metastasis, NOG could be promising molecular target in bone metastasis and that identifying small molecule inhibitors could aid in the treatment. Towards identifying cognate inhibitors of NOG, structure based virtual screen was employed. A total of 8.5 million ligands from e-molecule database were screened at a novel binding site on NOG identified by the Sitemap tool, employing GLIDE algorithm. Potential eight molecules were selected based on the Glide score, binding mode and H-bond interactions. Free energy of binding was calculated using Molecular mechanics based MMGBSA and the obtained energy was used in the prioritizing the compounds with the similar structures and glide score. Further, the compounds were evaluated for their druggability employing physico-chemical property analysis. Our study helped in identifying novel potential NOG inhibitors that can further be validated using in-vivo and in-vitro studies and these molecules can also be employed as tool compounds to study the functions of BMP.