1,7-Dideaza-2'-deoxy-6-nitronebularine: a pyrrolo[2,3-b]pyridine nucleoside with an intramolecular hydrogen bond stabilizing the syn conformation

Acta Crystallogr C. 2013 Aug;69(Pt 8):892-5. doi: 10.1107/S0108270113016922. Epub 2013 Jul 9.

Abstract

The title compound [systematic name: 1-(2-deoxy-β-D-erythro-pentofuranosyl)-4-nitro-1H-pyrrolo[2,3-b]pyridine], C₁₂H₁₃N₃O₅, forms an intramolecular hydrogen bond between the pyridine N atom as acceptor and the 5'-hydroxy group of the sugar residue as donor. Consequently, the N-glycosylic bond exhibits a syn conformation, with a χ torsion angle of 61.6 (2)°, and the pentofuranosyl residue adopts a C2'-endo envelope conformation (²E, S-type), with P = 162.1 (1)° and τm = 36.2 (1)°. The orientation of the exocyclic C4'-C5' bond is +sc (gauche, gauche), with a torsion angle γ = 49.1 (2)°. The title nucleoside forms an ordered and stacked three-dimensional network. The pyrrole ring of one layer faces the pyridine ring of an adjacent layer. Additionally, intermolecular O-H∙∙∙O and C-H∙∙∙O hydrogen bonds stabilize the crystal structure.

Keywords: crystal structure; disorder; nucleosides.

MeSH terms

  • Crystallography, X-Ray
  • Hydrogen Bonding
  • Models, Molecular
  • Nucleic Acid Conformation
  • Nucleosides / chemical synthesis
  • Nucleosides / chemistry*
  • Pyridines / chemical synthesis
  • Pyridines / chemistry*

Substances

  • Nucleosides
  • Pyridines