Crystal Structure of 2′-O-Succinyladenosine 3′,5′-(Cyclic)phosphate Monohydrate: A Model Compound to Study Protein–Nucleic Acid Interactions

Abstract

Abstract The crystal and molecular structure of 2′-O-succinyladenosine 3′,5′-(cyclic)phosphate monohydrate has been determined by X-ray diffraction techniques. The compound crystallizes in the orthorhombic space group P212121; Z=4 with a=5.633(1), b=15.853(2), c=20.607(3) Å. The final R value is 0.029. The adenine base is protonated at N(1). The base is in syn conformation (χ=−95.8°) with respect to the sugar, which has a C(3′)-endo-C(4′)-exo pucker (4T3). A six-membered ring formed by phosphate group and ribose shows chair conformation. The succinic acid moiety, which resembles side chains of certain amino acids, is found to have a bent skeleton. The cyclic AMP, which is known to play diverse roles in many metabolic processes, forms the nucleotide portion of the title compound. The succinic acid moiety that is covalently linked to this nucleotide in the present compound, shows direct and water mediated interactions with phosphate and base nitrogens of the nucleotide respectively. Such compounds can therefore serve as models to study the protein–nucleic acid interactions, which play a central role in many of the biological processes.