Drug-induced long QT syndrome has been principally ascribed to block of the cardiac hERG K(+) channel. Methanesulfonanilides, such as MK-499, E-4031 and dofetilide, are potent hERG antagonists that likely bind along the S6 helix within the inner vestibule of the pore. To further investigate these interactions, we broadly explored the structure-activity relationships of closely related analogs of MK-499 using a high-throughput ion flux assay, and evaluated in greater detail using patch-clamp electrophysiology. We observed that substitutions at the 4-position on the benzopyran ring significantly affected the potency of these analogs with the rank order of unsubstituted approximately ketone>amine>hydroxyl, implicating an important interaction at this position. We also evaluated the potency of these analogs on an S6 mutant of hERG (F656A) previously shown to significantly reduce the affinity for MK-499 and other known hERG antagonists (e.g. cisapride, terfenadine). In contrast to MK-499 (4-hydroxyl) and either the amine or unsubstituted analogs, the potency of the ketone analog was unaffected by this mutation suggesting that a compensatory interaction may be unveiled with the aromatic to apolar substitution, possibly through hydrogen bonding with Ser624 based on molecular modeling. More significantly, we found that this mutation rendered hERG susceptible to block in the closed-state by the smaller, unsubstituted analog, but not by MK-499 or larger analogs. Together these data suggest that interaction with Phe656 is not an absolute requirement for the binding of all methanesulfonanilide compounds, and that this residue may play a broader role in regulating access to the inner vestibule.