This is an annotated database that contains the 3D structural information of more than 120 entries of monosaccharides. These monosaccharides the alphabet of the building blocks of the vast majority of oligosaccharides, complex carbohydrates such as “glycan determinants” (blood group antigens, core structures, fucosylated oligosaccharides, sialylated oligosaccharides, Lewis antigens, GPI-anchors, N-and O- linked oligosaccharides, globosides,…), glycosaminoglycans, plants and, algal polysaccharides, as well as some bacterial polysaccharides.
There exists several ways of encoding and representing glycans. While maintaining the spirit of using the symbolic representation for monosaccharides (and towards glycans) this set of rules provides the necessary extension to the construction of three-dimensional structures, allowing encoding for computational manipulation. A detailed description of these is available within the chaper entitled: “Symbolic Representation of Monosaccharides in the Age of Glycobiology” http://www.glycopedia.eu . It is possible to concatenate the symbolic representation of monosaccharides with a limited number of structural descriptors to achieve a fairly exhaustive and comprehensive nomenclature which can be further used in constructing three dimensional structures of glycans.
This can be achieved using the following set
Residue Letter Name: Rib, Ara, Xyl, Lyx, All, Alt, Glc, Man, Gul, Ido, Gal, Tal,….and abbreviated trivial name.
[O-ester and ethers]: (when present) are shown attached to the symbol with a number, e.g.
6Ac for 6-O-acetyl group
3S for 3-O-sulfate group
3P for 6-O-phosphate group
6Me for 6-O-Methyl group
36Anh for 3-6 Anhydro
Pyr for Pyruvate
Absolute Configuration: D or L The D-configuration for monosaccharide and the L configuration for Fucose and Idose are implicit and does not appear in the symbol. Otherwise the L configuration, is indicated in the symbol, as in the case of Arabinose or L Galactose.
For those occurring in the furanose form, a letter N or S in inserted in the symbol, indicating the northern (N) or Southern (S) conformation of the five membered ring.
Anomeric configuration: The nature of the glycosidic configuration (α or β) is explicitly set within the symbol.
Ring conformation: All pyranoses in the D-configuration are assumed to have 4C1 chair conformation; those in the L configuration are assumed to have 1C4 chair conformation. Otherwise, the ring conformation is indicated in the symbol, as 2S0 in the case of α-L-Idopyranose. N or S indicates the conformation of the five membered rings on the conformational wheel.
The following table gives the content of the data base as per September 2013.
For establishing the 3D data base, they all have been subjected to systematic conformational sampling to determine their conformational preferences, using molecular mechanics optimization. Whereas most of the monosaccharides exhibit a fairly rigid ring conformation some cases exist such as in the case of iduronic acid, idose, and all furanosides where several ring shapes can occur. In these cases, the low energy conformations are available for each entry.