Talk:Syn/anti lateral protonation

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Click the "+" tab to add a new discussion section... Harry Brumer 11:10, 9 November 2009 (UTC)

Page created 2009-11-09

Table outline created for further modification. Harry Brumer 11:12, 9 November 2009 (UTC)

Three questions from Wim

Adding clan info

1) May I add the clan to the family (so the first row would be called Family / Clan and the first entry would then be GH1 / A)? Because this would be very usefull if I would (later) also introduce family-entries "by similarity" (for which there is as yet no proving complexed structure) just like Heightman&Vasella did in their table, e.g. all families of clan-A are anti by similarity.

I think this is a good idea, but the clan should be entered as a separate column, so the table can be sorted by Clan (where available). Harry Brumer 14:47, 9 November 2009 (UTC)

Wim - Great idea. Where clan is unknown, you could write 'unknown'!Spencer Williams 10:17, 10 November 2009 (UTC)

alpha/beta vs. axial/equatorial

2) At the second row (Anomeric specificity), may I add to the entries whether it is axial or equatorial? Because alpha / beta is by IUPAC-definition only for the anomeric versus D/L relationship within the Fisher projection and nothing else, thus alpha / beta is (often but) not always resp axial / equatorial in the sugar's ground state conformation, the prime example being glycosides of sialic/neuraminic acid where their ground state 2C5 is alpha-equatorial.

I would suggest we stick with alpha/beta for now, since it works in 95+% of the cases (although the limitation is acknowledged). Mike's e/a notation never really achieved widespread use, and the specialist will understand the odd cases. It's best to keep things simple in the beginning. Harry Brumer 14:47, 9 November 2009 (UTC)

Perhaps another column could be added for a->a, a->e, e->a, e->e. But I agree with Harry - Sinnott's notation is excellent but not often used.Spencer Williams 10:17, 10 November 2009 (UTC)

I can actually easily add an extra column with Michael's e/a notation, I tried this on a preview and it looks OK (I did not post it). It would be next to "Anomeric specificity" and could be called "Anomeric change". When I'll reach the neuraminidases, then I really think that we'll have to do this, since CAZypedia will certainly get visitors that do not know that alpha/beta is for the Fisher projection only, thus may wrongly assume that their alpha-aglycon is axial in the ground state. By the way, GH-9 is very clearly a syn protonator if I re-check pdb 4tf4 (changed). Added an entry for GH-2 and it looks fine. Wim Nerinckx 21:54, 11 November 2009 (UTC)

exo-anomeric column

The third question - but not for now - is to consider to add an extra row next to the one of the ligand, indicating if it is in or out of the exo-anomeric effect. Once I'll make-post the drawings, it will be very clear that in-anti and out-syn are connected, and indeed you can see this in several complexed structures.

Let's keep this idea on hold for a bit. Harry Brumer 14:47, 9 November 2009 (UTC)

I too agree with Harry. Let's try to get a fully consistent table up with well-recognized and accepted data/analysis. Less well-established/accepted theories should stand the test of publication in the open literature before being added to this encyclopedia.Spencer Williams 10:17, 10 November 2009 (UTC)

fold column

I figured out how to insert greek letters. Because I think that a nice completeness-info-addition to the table is to also add the fold for each family. If OK for you both then I do that. Wim Nerinckx 22:38, 10 November 2009 (UTC)

I think that's a good idea; as far as I'm concerned go ahead. Harry Brumer 07:07, 11 November 2009 (UTC)