The successful development of a number of HIV-1 protease (PR) inhibitors for the treatment of AIDS has validated the utilization of retroviral PRs as drug targets and necessitated their detailed structural study. Here we report the structure of a complex of human T cell leukemia virus type 1 (HTLV-1) PR with a substratebased inhibitor bound in subsites P5 through P5 . Although HTLV-1 PR exhibits an overall fold similar to other retroviral PRs, significant structural differences are present in several loop areas, which include the functionally important flaps, previously considered to be structurally highly conserved. Potential key residues responsible for the resistance of HTLV-1 PR to anti-HIV drugs are identified. We expect that the knowledge accumulated during the development of anti-HIV drugs, particularly in overcoming drug resistance, will help in designing a novel class of antileukemia drugs targeting HTLV-1 PR and in predicting their drug-resistance profile. The structure presented here can be used as a starting point for the development of such anticancer therapies.inhibitor ͉ leukemia ͉ retroviral protease H uman T cell leukemia virus type 1 (HTLV-1) is a retrovirus that is epidemiologically associated with mature CD3 ϩ CD4 ϩ T cell-type leukemia͞lymphoma (ATL), as well as with tropical spastic paraparesis͞myelopathy (1, 2). It is estimated that up to 30 million people worldwide are infected with HTLV, with ATL being particularly prevalent in Japan (3). Only an estimated 3-5% of people infected with the virus develop ATL in their lifetime, but for those that do, the prognosis is poor (4). Although a number of treatments for ATL, such as combination chemotherapy, monoclonal antibodies directed against the ␣ chain of the interleukin 2 receptor, and antiviral therapy involving IFN-␣ and zidovudine, are used clinically, they show only very limited efficacy (3). Novel approaches under investigation use proteasome inhibitors (5) and Tax-targeted immunotherapy (4), but they have not yet been tested in practice. It is clear that new anti-ATL targets need to be found.In common with other retroviruses, HTLV-1 encodes a protease (PR) necessary for its maturation. Because inhibition of the enzyme has been shown to prevent viral proliferation, development of inhibitors targeting HTLV-1 PR is an attractive new path for chemotherapy (6). HTLV-1 PR is a homodimer, with each chain containing 125 residues. The enzymatic properties of HTLV-1 PR, including its substrate specificity, have already been studied in considerable detail (7,8). Although the design and synthesis of inhibitors specific for HTLV-1 PR have been carried out, most of the compounds are active only in micromolar concentration (9, 10). The best statine-containing inhibitor has a K i of 50 nM under high-salt conditions (7) but of only 2.3 M in a low-salt buffer (11). In comparison, a number of subpicomolar inhibitors of HIV-1 PR have been developed by using the principles of rational drug design (12).Structural investigations of HTLV-1 PR have not been su...