5-Ethynyl-2′-de­oxy­cytidine: a DNA building block with a `clickable' side chain

The title compound [systematic name: 4-amino-1-(2-de­oxy-β-D-erythro-pentofuranos­yl)-5-ethynylpyrimidin-2(1H)-one], C₁₁H₁₃N₃O₄, shows two conformations in the crystalline state. The N-glycosylic bonds of both conformers adopt similar conformations, with χ = −149.2 (1)° for conformer (I-1) and −151.4 (1)° for conformer (I-2), both in the anti range. The sugar residue of (I-1) shows a C2′-endo envelope conformation (²E, S-type), with P = 164.7 (1)° and τ_m = 36.9 (1)°, while (I-2) shows a major C3′-exo sugar pucker (C3′-exo-C2′-endo, ₃T², S-type), with P = 189.2 (1)° and τ_m = 33.3 (1)°. Both conformers participate in the formation of a layered three-dimensional crystal structure with a chain-like arrangement of the conformers. The ethynyl groups do not participate in hydrogen bonding, but are arranged in proximal positions.