Merbarone is a selective human topoisomerase IIalpha inhibitor, which blocks human topoisomerase IIalpha (hTopoIIalpha)-mediated DNA cleavage. The binding site for merbarone was identified using molecular modeling studies. This homology modeled structure represents the macromolecular complex containing hTopoIIalpha (central domain and C-terminal domain), DNA (uncleaved) and merbarone (complexed at both the merbarone-binding sites).