The structure of 4-amino-1-[4-amino-2-oxo-1(2H)-pyrimidinyl]-1,4-dideoxy-β-D-glucopyranuronic acid (C-substance) monohydrate: a nucleoside fragment of gougerotin

Abstract

C-substance, the nucleoside fragment of the aminoacyl antibiotic gougerotin, crystallizes in space group P21 with cell dimensions a = 10.027 (5), b = 8.606 (3), c = 14.620 (7) A, fl = 98.45 (2)°; Z = 4. The structure was solved by direct methods and refined to an R index of 0-048 using 1987 intensities measured on a diffractometer. The two independent molecules are related by a pseudo twofold screw axis parallel to the z direction and have similar conformations, except for the orientation of the carboxyl group. The cytosine base is slightly nonplanar in both molecules with a shallow boat configuration. The pyranosyl-ring conformations are 4C 1 and the dispositions of the bases are anti, X = 75.0 (6)and 71.7 (5) ° for molecules A and B respectively. The two endocyclic C O bonds of the pyranose rings are equal in both molecules with a shortened base-sugar glycosyl C(I ')--N(1) bond, a feature reminiscent of the anomeric effect observed in glucosides with an equatorial substituent at C(I ') . The carboxyl groups are rotated differently about the exocyclic C(5 ' ) -C(6 ' ) bonds in the two molecules. In molecule B the carboxyl group is virtually in the plane of the ring 0(5 ' ) atom by virtue of a strong intramolecular hydrogen bond to the amino group, while in molecule A it is rotated into the plane of the ring C(4') atom by a hydrogen bond through a water to the carbonyl oxygen 0(2) of the base. Both molecules exist as zwitterions with a protonated amino group at the 4' position and an ionized carboxyl group. The structure also exhibits two bifurcated hydrogen bonds and a short intermolecular C(6) . . . 0(5 ' ) contact (3.01 A).