dan2097
t-Butyl N-(1-oxo-4-nitroisoindolin-2-yl)-L-glutamine interpreted different from ChemDraw (and what the authors intended)
In some of Cellgene's patents (WO1998003502A1_0102) for lenalidomide they use
t-Butyl N-(1-oxo-4-nitroisoindolin-2-yl)-L-glutamine
(with the 1 as an I) to represent
O=C1N(CC2=C(C=CC=C12)[N+](=O)[O-])[C@H](C(=O)OC(C)(C)C)CCC(=O)N
ChemDraw 19.1 recognises this name.
ChemSrc also uses this name:
https://www.chemsrc.com/en/cas/202271-82-7_1235814.html
Opsin gives
C(C)(C)(C)N([C@@H](CCC(N)=O)C(=O)O)N1C(C2=CC=CC(=C2C1)[N+](=O)[O-])=O
for that name, i.e., there is an extra N, and the t-Bu group defaulting to the extra N, rather than the acid group of glutamine.
Using t-butyl 2-(1-oxo-4-nitroisoindolin-2-yl)-L-5-amino-5-oxopentanoate in Opsin I get the intended structure.
I think Opsin is doing the right thing here, the name in the patent indicates an additional nitrogen. Though it appears that the alternative name has some uptake.
I will add it as an exception in our dictionaries, put thought you would like to be aware of the alternative interpretation.
Chemdraw roundtrips to tert-butyl (S)-5-(lambda^1-azaneyl)-2-(4-nitro-1-oxoisoindolin-2-yl)-5-oxopentanoate which is better than what I came up with above. After stripping out the lambda^1, Opsin is happy.
If I'm understanding correctly, ChemSrc also has the "wrong" structure? (extra nitrogen) I don't think it's possible for OPSIN to ignore the extra nitrogen without the potential for breaking other names. The t-Butyl implicitly forming an ester is more tractable, given the space in the name does somewhat imply it.
