Drawing a cyclic peptide and letter coding stereoisomers

Hi,

I have a couple of technical questions about MarvinSketch that perhaps
you can help me with, or point me to the right person for answers.

1) Is there an easy way to draw a cyclic peptide in using amino-acid single or triple letter codes?

2) Are stereo-isomers of amino-acids recognized with letter codes, for
example how do I denote D-Cystein without having to draw the entire
structure?



Thanks,

Anna

Hello Anu,

Is there an easy way to draw a cyclic peptide in using amino-acid single or triple letter codes?

So far the simplest way to draw peptides is to first drawing a ring by typing ring6 (for a peptide with 6 amino acid residues), and exchanging the ring carbons to amino acids:

Step-by-step:

1. type ring6 and click the canvas. Right-click the ring and click ungroup.

2. type the 3-letter code of the amino acid (the aa is on the cursor now) and click the ring carbon. Repeat with all aminoacids.

 

Very important: always check amino acid sequence direction (for example, by ungrouping the molecule) before saving the structure.

For linear peptides, editing directly the Source (Edit menu) is the simplest way. Here, 1-letter code can be used, and it is case-sensitive.

Are stereo-isomers of amino-acids recognized with letter codes, for

example how do I denote D-Cystein without having to draw the entire

structure?

There is no direct way to call D-aminoacids, if used often, a set of custom templates should be created. To make D-aminoacids: just mirror a L-aa inserted from the template library.