An analogue of adenosine diphosphate (ADP), i.e. adenosine hypodiphosphate (AhDP), was synthesized and crystallized in the form of two sodium salts, Na₅(H₂AhDP)₃(HAhDP)·24H₂O and Na(H₄AhDP)(H₃AhDP)(H₂AhDP)₂·15H₂O, which were structurally characterized for a conformational comparison with ADP. Two adenine (Ade) hypodiphosphate salts, i.e. (AdeH)₂(H₂P₂O₆)·2H₂O and (AdeH)₂(H₂P₂O₆), were used as model systems to analyse nucleobase–hypodiphosphate inter­action modes.