Figure 12.2.3   Drug design figures

a.   Comparison of N-substituted peptoid and peptide structures


b.   Alignment of an R-group to different positions on a ring scaffold. For this type of scaffold, unlike the peptoid, it may be better to define the scaffold positions required for building a particular R-group as atomtype U (dummyatom), and include the scaffold as a fixed ligand.


c.    Comparison of designed N-substituted peptoid drug and peptide -bound complexes with srcSH3. The drug or peptide are in sticks, colored CPK. The protein is in spacefill; positions allowed to change rotamer are colored CPK. The carboxylate (asp) on the peptoid forms a salt bridge with the protein arginine, and fills a pocket filled by a proline in the peptide-bound structure. The phenol groups (tyr) on the ligand pack against the protein tyrosines. The first position (left-most) sidechain in both the peptide and peptoid are both the same (leu).