The X-ray diffraction analysis of a stereocontrolled heterochiral designed model peptide Boc-DPro-Thr-OMe (1) revealed the existence of an unusual folded molecular structure, stabilized via an effective unconventional CH…O type intramolecular hydrogen-bond, encompassing a noncovalent 12-membered ring-motif. Together with an uncommon type a disposition of the urethane moiety, the tightly folded topology is compounded with a cis-DPro imide-bond. The overall conformation is suggested to be the reminiscent of specific type VI β-turn structures, hitherto, characterized across the Aaa-cis-Pro peptide-bonds in globular proteins and polypeptides. The 13C NMR spectrum of 1 in an apolar CDCl3 environment revealed the presence of approximately an equal population of cis and trans isomers unexpectedly, analogous to Pro side-chain, the 13C NMR chemical-shifts of Thr Cβ-resonance is observed to be sensitive toward cis-trans isomerization. In conjunction with solid-state FT-IR spectral data, we established that a network of complex intermolecular hydrogen-bonds stabilize a self-complementary noncovalent helical hexagonal self-assembly and crystallographic supramolecular aggregate. The results incline us to highlight that the stabilization of cis-DPro peptide-bond in crystalline state may be driven by the favorable energy of formation of an unconventional weak CH…O intramolecular hydrogen-bond. © 2011 Wiley Periodicals, Inc. Biopolymers 97: 73–82, 2012.