Three-dimensional structure of APOBEC-2 and other structure models of APOBEC proteins obtained by computer modeling that bear similarity with a root-mean-square deviation (RMSD) of 2.0 with the APOBEC-2 monomer, dimer or tetramer. Uses of the three-dimensional structure of APOBEC-2 and models of APOBEC proteins particularly for structure-based drug design of compounds, peptides or mutant APOBEC proteins designed to treat Hyper-IgM-2 Syndrome, B cell lymphomas and lentivirus infections, particularly the human immunodeficiency virus (HIV) infection. Methods for identifying a compound that binds to any fragment of an APOBEC protein. The method includes obtaining the three dimensional structure of the APOBEC-2 monomer, dimer or tetramer and identifying or designing one or more compounds that bind, mimic, enhance, disrupt, or compete with interactions of APOBEC family proteins with themselves, their nucleic acid substrates and other cellular or viral proteins based on the three dimensional structure of the APOBEC-2 protein.