Adenosine hypodiphosphate ester, an analogue of ADP: analysis of the adenine-hypodiphosphate interaction mode in hypodiphosphate nucleotides and adenine salts

作者：Otreba Marta^*; Budzikur Daria; Gorecki Lukasz; Slepokura Katarzyna A^*

来源：Acta Crystallographica Section C-Structural Chemistry, 2018, 74(5): 571-+.

DOI：10.1107/S2053229618005089

• nucleotides
• adenosine hypodiphosphate esters
• ADP analogues
• adenine salts
• hypodiphosphate salts
• sodium salts
• nucleobase interactions
• crystal structure
• hypodiphosphoric acid
• adenosine diphosphate

Adenosine diphosphate (ADP) plays a crucial role in cell biochemistry, especially in metabolic pathways and energy storage. ADP itself, as well as many of its analogues, such as adenosine hypodiphosphate (AhDP), has been studied extensively, in particular in terms of enzymatic activity. However, structural studies in the solid state, especially for AhDP, are still missing. An analogue of ADP, i.e. adenosine hypodiphosphate ester, has been synthesized and characterized in the crystalline form as two hydrated sodium salts of 20: 3'-isopropylideneadenosine 5'-hypodiphosphate (H(3)AhDP, C13H19N5O9P2 for the neutral form), namely pentasodium tetrakis(2': 3'-isopropylideneadenosine 5'-hypodiphosphate) tetracosahydrate, 5Na(+).3C(13)H(18)N(5)O(9)P(2)(-).C13H17N5O9P22-.24H(2)O or Na-5 (H(2)AhDP)(3)(HAhDP).24H(2)O, (I), and sodium tetrakis(2':3'-isopropylideneadenosine 5'-hypodiphosphate) pentadecahydrate, Na+.C(13)H(20)N(5)O(9)P(2)(+)2C(13)H(18)N(5)O(9)P(2).C13H19N5O9P2.15H(2)O or Na(H(4)AhDP)(H(3)AhDP)( H(2)AhDP)(2).15H(2)O, (II). Crystal structure analyses of (I) and (II) reveal two nucleoside hypodiphosphate ions in the asymmetric units with different ionization states of the hypodiphosphate unit and adenine base. For all AhDP nucleotides, the same anti conformation about the N-glycosidic bond and similar puckering of the ribose ring have been found. AhDP geometry and interactions have been compared to ADP nucleotides deposited in the Cambridge Structural Database. The adenine-hypodiphosphate interactions, identified as defining nucleotide self-assembly, have been analysed in model systems, i.e. the adenine (Ade) salts of hypodiphosphoric acid, namely bis(adeninium) hypodiphosphate dihydrate, 2C(5)H(6)N(5)(+).H2P2O62-.2H(2)O or (AdeH)(2)(H2P2O6).2H(2)O, (III), and bis(adeninium) hypodiphosphate, 2C(5)H(6)N(5)(+).H2P2O62-or (AdeH)(2)(H2P2O6), (IV).

• 出版日期2018-5