The criteria currently followed for selecting antitumor compounds include agents that can target apoptosis inhibitor proteins and cancer cell markers. In silico studies are often used to identify suitable antitumor compounds for the cancer targets. The aim of the present study is to evaluate the interactions of some antitumor compounds reported from marine Streptomyces with cancer target proteins. Nine compounds were selected from marine Streptomyces based on previous reports and evaluated for their interactions with cancer target proteins by in silico molecular docking approach. Interactions of the selected ligand with target proteins were studied by PatchDock bioinformatics docking tool. Among the compounds tested marmycin A was interacted very effectively with human epidermal growth factor receptor 2 (HER2) and showed a least binding energy of -472.92 kcal/mol. The compound altemicidin showed a least binding energy of -415.66 kcal/mol with cyclin dependent kinase 4 (CDK4). The ligands resistoflavine and resistomycin also interacted with HER2 and showed the binding energy of -402.10 kcal/mol and -377.78 kcal/mol respectively. Other ligands proximycin A, chandrananimycin C, echinosporin, streptochlorin and streptokordin also showed the binding energy of -341.11 kcal/mol, -313.31 kcal/mol, -305.64 kcal/mol, -291.91 kcal/mol and 222.34 kcal/mol respectively with CDK4 protein. These results of our study suggest that HER2 and CDK4 are better cancer drug targets for therapy. © 2013 International Association of Scientists in the Interdisciplinary Areas and Springer-Verlag Berlin Heidelberg.