X-ray crystal and ab initio structures of 3′,5′-di-O-acetyl- N(4)-hydroxy-2′-deoxycytidine and its 5-fluoro analogue: Models of the N(4)-OH-dCMP and N(4)-OH-FdCMP molecules interacting with thymidylate synthase

Adam Jarmuła, Wojciech R. Rypniewski, Krzysztof Felczak, Wojciech Rode

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Abstract

The crystal and molecular structures of the 3′,5′-di-O-acetyl- N(4)-hydroxy-2′-deoxycytidine molecule and its 5-fluoro congener have been determined by X-ray single crystal diffraction. The 3′,5′-di-O- acetyl-N(4)-hydroxy-5-fluoro-2′-deoxycytidine molecule crystallizes in the space group C2 with the following unit cell parameters: a = 21.72 Å, b = 8.72 Å, c = 8.61 Å, and β = 90.42°. 3′,5′-di-O- acetyl-N(4)-hydroxy-2′-deoxycytidine also belongs to the monoclinic space group C2 and the unit cell parameters are: a = 39.54 Å, b = 8.72 Å, c = 22.89 Å, and β = 95.26°. The non-fluorine analogue demonstrates a rare example of crystal structure with five symmetry-independent molecules in the unit cell. All the molecules in both crystal structures have the sugar residue anti oriented with respect to the base, as well as have the N(4)-OH residue in cis conformation relatively to the N(3)-nitrogen atom. In addition to the molecular geometries from X-ray experiment, the optimized molecular geometries have been obtained with the use of theoretical ab initio calculations at the RHF/6-31G(d) level. The corresponding geometric parameters in the molecules of 3′,5′-di-O-acetyl-N(4)-hydroxy-2′- deoxycytidine and its 5-fluoro congener have been compared. The differences including the C(5)=C(6) bond shortening and C(4)-C(5)-C(6) angle widening in the fluorine analogue are discussed in this paper in relation to the molecular mechanism of enzyme, thymidylate synthase, inhibition by N(4)-hydroxy-2′- deoxycytidine monophosphate and its 5-fluoro congener.

Original languageEnglish (US)
Pages (from-to)541-549
Number of pages9
JournalStructural Chemistry
Volume16
Issue number5
DOIs
StatePublished - Oct 1 2005
Externally publishedYes

Keywords

  • Ab initio structure
  • Crystal structure
  • Nucleoside analogues of N(4)-OH-dCMP and N(4)-OH-FdCMP
  • Thymidylate synthase

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