Elementary Patterns in Protein–Nucleic Acid Interactions. II. Crystal Structure of 3-(Adenin-9-yl)propionamide

Abstract

In order to study adenine-amide interactions, 3-(adenin-9-yl)propionamide has been synthesized and its crystal structure examined. The crystals are monoclinic, the space group being P21/a, with unit-cell dimensions of a=25.668 (1), b=8.025 (1), c=4.684 (1) Å, β=103.54 (1)°, and Z=4. The adenine bases are linked along the two-fold screw axis through the hydrogen bonds, N(6)H···N(1) and N(6)H···N(7). The amide group is hydrogen-bonded to N(3) of adjacent adenine moiety, the distance NH···N(3) being 3.055 Å. The model fitting by computer graphics indicates that this binding scheme could be an elementary interaction pattern between the amide group in protein and adenine in the minor groove of double helical DNA.

Elementary patterns in protein–nucleic acid interactions. VII. Structure of N-[3-(9-adeninyl)propionyl]-DL-tryptophan ethyl ester, C21H23N7O3

“…1. The bond distances and angles are in agreement with those found in 3-(9-adeninyl)propionamide (Takimoto, Takenaka & Sasada, 1981), 3-(9-adeninyl)propionamide: lmethylthymine (l:l) complex dihydrate (Takimoto, Takenaka & Sasada, 1982), 3-(7-adeninyl)-propionamide monohydrate (Takimoto, Takenaka & Sasada, 1983), L-tryptophan hydrochloride (Takigawa, Ashida, Sasada & Kakudo, 1966) and OL-tryptophan ethyl ester hydrochloride (Vijayalakshmi & Srinivasan, 1975). The molecule is extended so that there is no intramolecular stacking between the two rings; the torsion angles being given in Fig.…”

Structure of 9-{2-[(4-imidazolyl)methylthio]ethyl}adenine

“…1 shows the conformation of the molecule with the atom numbering, bond distances and angles. The dimensions of the adenine moiety, the imidazolyl group and the linking part [from C(11) to C(6')] are in good agreement with those in the related compounds (Kistenmacher & Rossi, 1977;Takimoto, Takenaka & Sasada, 1981;Edington & Harding, 1974;Madden, McGrandy & Seeman, 1972;Prout, Critchley, Ganellin & Mitchell, 1977). The molecule is folded and the torsion angles N(9)-C(11)-C(12)-S, C(11)-C(12)-S-C(6') and C(12)-S-C(6')-C(5') are 60.1 (5), 87.8 (4) and -62.4 (4) °, respectively.…”

“…The adenine moieties are arranged so as to form ribbons along the twofold screw axis through the N(6)H...N(7) and N(6)H...N(1) hydrogen bonds. Such a ribbon structure of adenines has often been found in crystals of adenine derivatives (e.g., Takimoto, Takenaka & Sasada, 1981). The imidazolyl groups are connected to each other along the e axis by the N(I')H...N(3') hydrogen bonds.…”

Contrasting Crystallographic Signatures of 9-Carboxypropyl Adeninium Cation: Adenine Dimerization vs Carboxylic Group Interaction

“…More specifically, presence of a carboxyl group in adenine might be considered as mimicry of adenine-aspartic/glutamic acid interaction, whereas a carboxamide in adenine could be considered as mimicry of adenine-asparagine/glutamine interaction. 14 Crystal lattice analysis of five adducts of protonated 9-(carboxypropyl)adenine provided an interesting preference of dimer formation and hydrogen bonding patterns. Type I pattern representing self-association of the adeninium cation was exhibited by two adducts, 1 and 2a, whereas the other three adducts, 2b, 3, and 4, displayed cross-dimerization by the interaction of adeninium cation with the carboxyl group, leading to the formation of infinite linear chains in the crystal lattice.…”