Calculating three-dimensional molecular structure of paliurine B from atom-atom distance and restrained energy minimization.

The conformation of paliurine B, a 13-membered cyclopeptide alkaloid isolated from Paliurus ramosissimus, has been determined from 2D NMR and distance geometry, followed by the restrained energy minimization calculation. The conformation of the 13-membered ring is well-defined but that of the acyclic dipeptide tail region is relatively disordered. In addition, the cavity in the 13-membered ring is just large enough to insert a magnesium ion but is a little small for calcium or sodium ions.