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Attached is the structure of one aminoglycosides, kanamycin. I understand that the ring binds to 4 position of 2-DOS is numbered with prime (') and sugar that links to 4 or 5 position of 2-DOS is numbered with double prime ('') but my question is how to do the numbering for 2-DOS (center ring). Can anyone teach me how? I have searched through Google and still have no idea on it. enter image description here

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    $\begingroup$ With biomolecules like these, I've often seen the numbering being chosen by convention rather than with IUPAC rules. I don't know anything about these systems, so I can't say for sure. $\endgroup$ – orthocresol Sep 26 '16 at 17:30
  • $\begingroup$ DOS is not an abbreviation I commonly come across. Can you include what it means, please? $\endgroup$ – Jan Sep 28 '16 at 14:42
  • $\begingroup$ deoxystreptamine $\endgroup$ – Curt F. Sep 28 '16 at 17:56

Like @orthocresol said in his comment, biomolecules are often numbered by convention. The 'traditional' numbering for 2-deoxystreptamine is shown below on the left, and IUPAC numbering (not used) is shown on the right:

enter image description here The most likely rationale for the traditional numbering is that the compound is a diamine so the numbering starts from one of the amino substituents and goes towards the other one.

EDIT: OK, now I understand exactly where lies your confusion. The molecule of 2-deoxystreptamine (2-DOS) has a plane of symmetry. If we are to number the molecule alone, it doesn't matter from which amine group we will start. But as you noticed, the kanamycin is asymmetrical and there are indeed two ways to number the ring of 2-DOS. To solve this problem, we need to look on the structures of other aminoglycosides and their biosynthetic pathway. Many of the antibiotics from this class are biosynthesized through an intermediate compound known as paromamine (I prefer Haworth projection):


The numbering is logical - if we would start from the other amine then the glucosamine substituent would be at atom 6 (against the usual rules of numbering where we prefer lower numbers for substituents). Most aminoglycosides can be divided into two groups: 4,5-disubstituted (neomycins, paromomycins) and 4,6-disubstituted (kanamycins among others). Therefore the red numbering in the original question is the right one, if we assume the synthetic pathway described in this article:

Park J.W. et al, "Discovery of parallel pathways of kanamycin biosynthesis allows antibiotic manipulation" Nat. Chem. Biol. 2011, 7(11):843-852 (DOI: 10.1038/nchembio.671).

  • $\begingroup$ If I were to have name it with a traditional way, which start from either one amine, I will be having 2 alternatives, one in blue and another in red (I have attached new photo on my original post). So if I were to follow the blue ones, I will have the left sugar at position 4 of 2-DOS I would name it with prime and the right sugar with double prime. However, if I were to use the red route, the left sugar would be numbered with double prime as it is now at position 6. BTW I got this numbering technique from here: bioscience.org/1999/v4/d/wright/fulltext.htm (2.0 Introduction) $\endgroup$ – Theresa Sep 28 '16 at 17:16

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