Crystal structure and conformation of 5-fluorouridine: conformational preferences for 5-fluorinated pyranosides.
Crystals of 5-fluorouridine (5FUrd) have unit cell dimensions a = 7.716(1), b = 5.861(2), c = 13.041(1)A, alpha = gamma = 90 degrees, beta = 96.70 degrees (1), space group P2(1), Z = 2, rho obs = 1.56 gm/c.c and rho calc = 1574 gm/c.c The crystal structure was determined with diffractometric data and refined to a final reliability index of 0.042 for the observed 2205 reflections (I > or = 3sigma). The nucleoside has the anti conformation [chi = 53.1(4) degrees] with the furanose ring in the favorite C2'-endo conformation. The conformation across the sugar exocyclic bond is g+, with values of 49.1(4) and -69.3(4) degrees for phi(theta c) and phi (infinity) respectively. The pseudorotational amplitude tau(m) is 34.5 (2) with a phase angle of 171.6(4) degrees. The crystal structure is stabilized by a network of N-H...O and O-H...O involving the N3 of the uracil base and the sugar 03' and 02' as donors and the 02 and 04 of the uracil base and 03' oxygen as acceptors respectively. Fluorine is neither involved in the hydrogen bonding nor in the stacking interactions. Our studies of several 5-fluorinated nucleosides show the following preferred conformational features: 1) the most favored anti conformation for the nucleoside [chi varies from -20 to + 60 degrees] 2) an inverse correlation between the glycosyl bond distance and the chi angle 3) a wide variation of conformations of the sugar ranging froni C2'-endo through C3'-endo to C4'-exo 4) the preferred g+ across the exocyclic C4'-C5' bond and 5) no role for the fluorine atom in the hydrogen bonding or base stacking interactions.
Soni
Sunil Dutta
SD
Department of Cancer Biology, Roswell Park Cancer Institute, Buffalo, New York 14263, USA.
Srikrishnan
Thamarapu
T
D000970:Antineoplastic Agents / Q000737:chemistry / Q000494:pharmacology; D018360:Crystallography, X-Ray; D006367:HeLa Cells; D006801:Humans; D006860:Hydrogen Bonding; D008958:Models, Molecular; D008968:Molecular Conformation; D011743:Pyrimidines / Q000737:chemistry; D013329:Structure-Activity Relationship; D014529:Uridine / Q000031:analogs & derivatives* / Q000737:chemistry* / Q000494:pharmacology
D000970:Antineoplastic Agents; D011743:Pyrimidines; C001943:5-fluorouridine; D014529:Uridine