Hsp90? and Hsp90? are implicated in a number of cancers and neurodegenerative disorders but the lack of selective pharmacological probes confounds efforts to identify their individual roles. Here, we analyzed the binding of an Hsp90?-selective PU compound, PU-11-trans, to the two cytosolic paralogs. We determined the co-crystal structures of Hsp90? and Hsp90? bound to PU-11-trans, as well as the structure of the apo Hsp90? NTD. The two inhibitor-bound structures reveal that Ser52, a nonconserved residue in the ATP binding pocket in Hsp90?, provides additional stability to PU-11-trans through a water-mediated hydrogen-bonding network. Mutation of Ser52 to alanine, as found in Hsp90?, alters the dissociation constant of Hsp90? for PU-11-trans to match that of Hsp90?. Our results provide a structural explanation for the binding preference of PU inhibitors for Hsp90? and demonstrate that the single nonconserved residue in the ATP-binding pocket may be exploited for ?/? selectivity.