Crystal and molecular structure of cyclic dodecadepsipeptide – cyclol-[-D-Val-D-Hyi-Val-Hyi-(D-Val-Hyi-Val-D-Hyi)2-]·2C3H6O
V. Z. Pletnev, I. N. Tsygannik, I. Yu. Mikhailova, V. T. Ivanov, D. A. Langs, P. Grochulski, W. L. Duax
Institute of Molecular Genetics, Academy of Sciences of the USSR, Moscow; M. M. Skemyakin Institute of Bioorganic Chemistry,
Academy of Sciences of the USSR, Moscow; Medical Foundation of Buffalo, Buffalo, USA
Abstract: The crystal structure of a synthetic analogue of meso-valinomycin, crystallized with two acetone molecules, has been solved by X-ray direct methods. The trigonal crystals belong to the P32 space group, with the number of molecules in the unit cell z=3, and cell dimensions a=b=15.2085 Ấ, c=29.3250 Ấ, α=β=90°, γ=120°. The standard (R) and weighted (Rω) factors after the structure refinement on atoms C, N, O in anisotropic thermal motion approximation and with the contribution from H atoms taken into account are 0,070 and 0,082, respectively.
The molecule adopts an asymmetric conformation stabilized by six amide intramolecular hydrogen bonds NH···OC of the 4→1 type; one of those is strong and the other are weakened in different extent. The side chains occupy the external pseudoaxial positions towards the cyclic frame of the molecule, whereas six free ester carbonyl groups have different orientations. In contrast to meso-valinomycin, the analogue under study has no specific binding site for metal ions. The isopropyl side chains of D-Hyi(2) and Hyi(4) residues effectively shield, from both sides, the access to the inner molecular cavity.
Russian Journal of Bioorganic Chemistry 1991, 17 (3):359-371