Background: New antibacterial compounds are urgently needed; DNA gyrase is a well-validated target.Results: Diospyrin and other naphthoquinones inhibit DNA gyrase by binding to a novel site in the B subunit.Conclusion: Naphthoquinones are inhibitors of gyrase with a novel mechanism of action.Significance: Naphthoquinones have potential as antibacterial compounds against TB.

New structures of the N-terminal 43 kDa fragment of the E. coli DNA gyrase B subunit reveal two discrete monovalent cation-binding sites that could have functional roles.

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