Crystal structures of 5-fluoro-dUrd and its 2 and/or 4-thio analogues: Models of substituted dUMP pyrimidine ring interacting with thymidylate synthase

Adam Jarmuła, Romana Anulewicz, Andrzej Leś, Michał K. Cyrański, Ludwik Adamowicz, Maria Bretner, Krzysztof Felczak, Tadeusz Kulikowski, Tadeusz M. Krygowski, Wojciech Rode

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13 Scopus citations


In order to understand the influence on thymidylate synthase interactions with dUMP analogues of the pyrimidine ring 2- and/or 4-thio, and 5-fluoro substitutions, X-ray diffractions by crystals of 5-fluoro-dUrd and its 2- and 4-thio, and 2,4-dithio analogues were measured, the four structures solved and refined. The following conclusions were suggested by results of comparative analyses of structural parameters (bond lengths, valence angles), followed by theoretical considerations based on calculated resonance structure distributions and aromaticity indices of the uracil, thiouracil, fluorouracil and fluorothiouracil rings. The effect of 4-thio substitution of FdUMP, altering specificity of inactivation of thymidylate synthases from various sources, is probably due to weaker proton acceptor power of the 4-thio substituent and increasing acidity (enhanced proton-donor power) of the N(3)-H moiety, resulting in an impaired fitness into the network of hydrogen bonds in the enzyme active center cleft. 2,4-Dithio substitution results in (i) impaired pyrimidine ring recognition by the enzyme active center, due to the 4-thio substituent (ii) increased pyrimidine ring aromaticity in dUMP, leading to resistance of C(6) to nucleophilic attack by the enzyme active center cysteine and (iii) altered planarity of the pyrimidine ring and deflections, with respect to the ring plane, of substituents at C(2), C(4) and C(5). 5-Fluoro substitution apparently activates the pyrimidine ring towards the interaction with thymidylate synthase by producing local strain, which results in an increased reactivity as predicted by the Walsh-Bent rule.

Original languageEnglish (US)
Pages (from-to)277-286
Number of pages10
JournalBiochimica et Biophysica Acta - Protein Structure and Molecular Enzymology
Issue number2
StatePublished - Feb 17 1998
Externally publishedYes

Bibliographical note

Funding Information:
Supported by the State Committee for Scientific Research – Grant No. 267/T09/95/08. M.K. Cyrański is a holder of a grant from the Polish Science Foundation.


  • Aromaticity
  • DUMP analogue
  • Thymidylate synthase
  • Walsh-Bent rule
  • X-ray diffraction

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