Molecular and crystal structure of 1-(3'-C-methyl-2'-deoxyribofuranosyl)thymine

A. V. Bochkarev, G. V. Gurskaya, A. S. Zdanov, E. M. Kazmina, I. I. Fedorov

V. A. Engelhardt Institute of Molecular Biology, Academy of Sciences of the USSR, Moscow; I. M. Sechenov Moscow Medical Academy, Moscow

Abstract: The structure of 3'-C-methylthymidine (3'-Me-Thd), a “functionally competent” analogue of thymidine, was determined by X-ray analysis. The space group is P2₁. Cell dimensions are: a=5.100(1), b=12.489(2), c=9.202(1) A; β=98.47(1)°, V=579.7 A³, Z=2. The structure was elucidated by direct methods and refined by the full-matrix least square method to R=2.3%. The molecule of 3'-Me-Thd has anti-con-formation with respect to the glycosidic bond (χ(04'–C1'–N1–C2)=-116.6°), C2'-endo-C1'-exo puckering of the sugar moiety and gauche-gauche conformation about exocyclic C4'–C5'-bond (φ(C3'–C4'–C5'–05')=50.1°). Using comparative analysis of 3'-Me-Thd and 3'-Me-cytidine [1] it was concluded that 3'-Me-pyrimidines have “hard” conformation independent of the sugar and base types.

Russian Journal of Bioorganic Chemistry 1991, 17 (8):1094-1100

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