[AMBER] Help with carbohydrate nomenclature

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Thu, 7 Oct 2021 19:09:28 -0400

Hi All,

I'm hoping someone can shed some light on an issue that's been bugging
me for a while about determining alpha/beta forms of carbohydrates in
cyclic form.

So I get that there is the anomeric carbon (carbon bearing
hemiacetal/acetal, typically C1/C2), the anomeric reference carbon
(which I think is the highest stereocenter in the ring) and the
configurational carbon (highest numbered stereocenter). The
configuration around the configurational carbon determines D/L, and as
I understand it _the relative orientation of the oxygen on the
anomeric carbon to the oxygen on the anomeric reference carbon_
determines alpha/beta (see e.g.
Specifically, if they are on the same side that's beta, and opposite
is alpha.

This seems to hold for most sugars. Take for example
alpha-D-glucopyranuronic acid (https://www.rcsb.org/ligand/GCU). Here
the orientation of the O at the anomeric carbon (C1) and the anomeric
reference carbon (C5) are clearly opposite, hence alpha. However, take
as another example alpha-D-xylopyranose
(https://www.rcsb.org/ligand/XYS). Now, assuming I'm correct in that
the anomeric carbon is C1 and the anomeric reference is C4 (which
appears to be the highest numbered stereocenter), the oxygens bound
are clearly pointing in the same direction. And for the beta
(https://www.rcsb.org/ligand/XYP) they are on opposite sides.

Now I'm sure I'm just not understanding the nomenclature correctly (or
making some other obvious mistake), but I just can't seem to wrap my
head around why XYS is alpha and XYP viceversa, when for almost every
other sugar I've looked at it's been the other way (opposite=alpha,
same=beta). Can anyone explain this?

Thanks, and sorry for the long post!


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Received on Thu Oct 07 2021 - 16:30:02 PDT
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