This data base contains the NMR spectra that have
been recorded and interpreted for more than 150 bioactive oligosaccharides
(referred to as “glycan determinants”).
These glycan determinants are recognized by glycan-binding proteins;
these include lectins, receptors, toxins, microbial adhesins, antibodies,
enzymes. These glycan determinants have been systematically organized
using standard names in the field of carbohydrate research into 31
categories and sub-categories :
Gal a1-3Gal oligosaccharides (Galili and xeno antigens, Isogloboseries)
Gal a1-4Gal oligosaccharides
Ganglioside sugars
Globoside sugars (P antigens) (Globo series - core structure type 4, P blood group antigens and analogues, Stage-specific Embryonic antigens )
Glucuronylated oligosaccharides
Isoforssman antigen
Lewis antigens
Sialyl Lewis A, Sialyl Lewis X
Sialylated oligosaccharides (type 1, type 2)
Trehalose-like sugars
Xeno Lewis A, Xeno Lewis X
Provision is made to create new sub-families.
Data Query
The database is available from Glyco3D.
Upon reaching the search page, two buttons to query the data base
appear on the left hand panel: Simple search and Advanced search.
Simple Search
A search box is provided, in which the user selects from the name of the oligosaccharide of
interest, available through a drop-down button that enlists all the oligosaccharides
present in the data base. The selection involves first a choice of the family and
second the choice of the sub-family.
The result indicates the sequence of the repeating unit of the oligosaccharide, following the nomenclature established for the Glyco3D portal.
Advanced Search
Upon selecting “Select Criteria”, two search boxes appear offering the choice between
the sequence of the repeating unit and the method of investigation used in the
determination of the 3D structure. Selecting the “sequence option” opens a drop-down
button that enlists all the sequences present in the data base.
The user may want to combine the two selection criteria.
Molecule Information
This includes the trivial name of the glycan,
its sequence, its type of constituent, its category and the experimental
conditions used to collect the NMR spectra (Temperature, Solvent,
Frequency, Concentration).
Display and Download
The graphical representation of the
stereochemical configuration and the symbolic notation for carbohydrates
are provided. The 1H- and 13C-NMR spectra are given along with the
assignments of the hydrogen and carbon atoms, respectively.
Depending upon the cases, COSY, TOCSY, HMQC and HMBC experiments are also
shown. Provision is given to download the spectra for further use.