Interaction between the E2 protein and E1 helicase of human papillomaviruses (HPVs) is essential for the initiation of viral DNA replication. We recently described a series of small molecules that bind to the N-terminal transactivation domain (TAD) of HPV type 11 E2 and inhibits its interaction with E1 in vitro and in cellular assays. Here we report the crystal structures of both the HPV11 TAD and of a complex between this domain and an inhibitor, at 2.5-and 2.4-Å resolution, respectively. The HPV11 TAD structure is very similar to that of the analogous domain of HPV16. Inhibitor binding caused no significant alteration of the protein backbone, but movements of several amino acid side chains at the binding site, in particular those of Tyr-19, His-32, Leu-94, and Glu-100, resulted in the formation of a deep hydrophobic pocket that accommodates the indandione moiety of the inhibitor. Mutational analysis provides functional evidence for specific interactions between Tyr-19 and E1 and between His-32 and the inhibitor. A second inhibitor molecule is also present at the binding pocket. Although evidence is presented that this second molecule makes only weak interactions with the protein and is likely an artifact of crystallization, its presence defines additional regions of the binding pocket that could be exploited to design more potent inhibitors.Human papillomaviruses (HPVs) 1 are the etiological agents of malignant and benign lesions of the differentiating squamous or mucosal epithelium, notably of cervical cancer. Approximately 25 HPV types replicate in mucosal tissues of the anogenital tract. HPV16, -18, and -31 are the most prevalent "high-risk" types found in pre-cancerous or malignant lesions of the cervix. HPV6 and -11 are the most common "low-risk" types, which cause benign genital warts (condyloma acuminata), a less serious condition but one of the most common sexually transmitted diseases (1). Currently, no specific antivirals are available for the treatment of HPV infections.The small circular double-stranded DNA genome of papillomavirus is actively maintained as a multicopy episome in the nucleus of infected epithelial cells. This process is dependent on replication of the viral genome by the viral E1 and E2 proteins, in conjunction with the host DNA replication machinery. E2 is a sequence-specific DNA-binding protein that has a number of functions in the viral lifecycle. In addition to its role in the initiation of viral DNA replication, E2 is involved in regulating the transcription of viral genes (2-7), and in the segregation of the viral genome during cell division (8, 9). As a replication initiation factor, E2 binds with high affinity to specific sites located within the viral origin (ori) to help recruit it to the E1 helicase (10 -13). Formation of a ternary complex between E1, E2, and the origin relies not only on the interaction of E1 and E2 with specific DNA sequences at the origin but is also critically dependent on a direct interaction between these two proteins (14 -18).The 40-kDa E2 prote...