Cytidine, crystal structure

Fig. 12.—The Crystal Structure of Cytidine, with the Pyrimidine King Shown in Heavy Lines. (Adapted from Furberg.141)...

Cyclic Trimer Configuration. The a-cytidine [ACYTID] crystal structure contains two cyclic trimer configurations (Fig. 17.32). In one, N(H)H is engaged in a three-center bond, the other is a homodromic cycle stabilized by a- and w-cooperativity. A comparable situation is found in the crystal structure of a-pseudouridine monohydrate [APSURD] (Fig. 17.13). The glycosyl link is to uracil C(6) instead of N(l), and therefore the N(1)H group is free to donate a hydrogen bond in a homodromic cycle. 

If the crystal structures and hydrogen-bonding patterns of uridine and thymidine and their simpler derivatives are compared with those of cytidine, it becomes obvious that the -NH2 functional group has a characteristic influence. The nucleosides without the -NH2 groups have less than average hydrated crystals, although the one nucleotide represented, uridine-3 -monophosphate, crystallizes as a monohydrate. 

Selected crystal structures of cytidlne and its derivatives. The cytidine-related nucleoside and nucleotide crystal structures for which reliable hydrogen-bond patterns can be reported include five nucleotides. Amongst the nucleotides there is more variety than with the uridine compounds. There are three hydrates, four hydrochlorides, and a nitrate. The conjugated NH2 group is always involved as a donor, but never as an acceptor. Several different configurations are observed ... 

The crystal structure of cytidine-3 -phosphate (monoclinic) [CYTIAC01]... 

Rosenberg JM, Seeman NC, Day RO, Rich A (1976) RNA double-helical fragment at atomic resolution. II. The crystal structure of sodium guanylyl-3, 5 -cytidine monohydrate. J Mol Biol 104 145-167... 

The crystal structure of l-(/3-D-erythrofuranosyl)cytidine, the des(hydroxymethyl) analog of /3-cytidine, has been determined and used to correlate the preferred conformations of furanoses in solution with those in the solid state. Conformational similarities and differences of tetrofuranoses vs. pentofuranoses have been charted as well <2007AXCol37>. 

The aminoaqfl-4-aminohexosyl-cytosine group of antibiotics is classified based on chemical structures (Fig. 4.11) each of which contains a cytosine base. Included in this group are blasticidin S, gougerotin, amicetin and bamicetin [46]. These antibiotics are not used therapeutically. However blasticidin S is an important antifungal used on rice crops. Only the crystal structure of blasticidin S bound to the ribosome is available. The chemical structure of blasticidin S resembles that of pep-tidyl-cytidine, although not as closely as puromycin resembles a tyrosylated adenosine (Fig. 4.11). 

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