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Quote from: Studentofstuff123 on June 03, 2013, 03:58:06 AMAfter reading the list provided, I'm thinking it could be hemiaminal, but that has 5 R groups. Is it a hemiaminal?The specific linkage in the red box is a hemiaminal - not sure where you are getting 5 R groups from:You have in this case:R1 = sugar ring; R2 = sugar ring; R3 = Asn residue of peptideMore specifically (also considering what is outside the red box) you could call this structure an N-acyl hemiaminal (because R3 is an acyl group). Based on the core amide structure:and given that R1 = glycosyl, you could call it an N-glycosyl amide. There are a lot of functional groups present, so there is more than one logical way of describing what is present.
After reading the list provided, I'm thinking it could be hemiaminal, but that has 5 R groups. Is it a hemiaminal?
Quote from: Kikko on June 02, 2013, 06:10:53 AMIs it a tertiary amine ?No, look it up: example of a list I found on google.In your original post you highlighted this fragment:
Is it a tertiary amine ?
OK, so ... removing all the rest of the graphic, and drawing it out, (and converting to SMILES so it displays here,)Is that sort of close to it -- ignoring that the rest of the sugar ring has to be called a CH3 (I'm not very good at SMILES yet)? Like everyone else, I see a couple of functional groups, but I don't know a name for this one by itself. Unless the letters for the atoms spell your school's initials, or something. Could that be it?
@OP, You must make an attempt; that is a forum rule. However, I will give you a hint. The functional group that connects a base (purine or pyrimidine) to a ribose or deoxyribose in RNA or DNA respectively, is similar.
Looking back at it, I am not sure where you get your "fragment".I can understand the R3 group.But what is R1 and R2 ? One of them has to be the sugar group where N is linked to (and contains the "red O", but the other R? Isnt Arkcon his figure better?
Quote from: Kikko on June 03, 2013, 05:26:01 AMLooking back at it, I am not sure where you get your "fragment".I can understand the R3 group.But what is R1 and R2 ? One of them has to be the sugar group where N is linked to (and contains the "red O", but the other R? Isnt Arkcon his figure better?This is what I did:
Well, R1 and R2 are by definition anything, since the O.P. drew a red box to exclude much of the ring. Its a bit confusing, since in the original molecule, what ends up as R1 and R2 are parts of the same ring, but the question isn't about that.
It is common to refer to the linkage between a base and the (deoxy)ribose in RNA or DNA as an N-glycoside. However, this is frowned upon in some circles. "...however the use of 'N-glycoside', although widespread in biochemical literature, is improper and not recommended here ('glycosylamine' is a perfectly acceptable term)." One wonders whether the present group might be called a glycosylamide. http://www.chem.qmul.ac.uk/iupac/2carb/33.html
ALso: if I look up the definition of Glycosidic bond, I see it refers to having a hemiacetal group and this is not the case in DNA so I wonder where they came up with this glycosidic bond.
He confirmed that it was indeed correct, hemiaminal ether more specifically
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