What molecules can I build using GLYCAM?

Answer in progress….

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The tables below list the current capabilities of the GLYCAM-Web parameter sets.

Note: these capabilities might differ slightly from those of the point-and-click builder.  They should mostly work using the text and URI (URL) builders.

Tables in this document:

  1. Glycan residues available
  2. Reducing-end aglycon residues available
  3. Derivative residues available.
  4. Common synonymous abbreviations

Table 1: Glycan Availability Table

Table Legend:

  • TLC = the “three-letter” code commonly used as an abbreviation for the residue. Note that these are not always three letters in length. But, most are.
  • GC = the GLYCAM one- or two-letter code, “none” if there is none.
  • Ready = Yes or no: Is this residue currently available?
    • Residues due to be released soon are included in this manner.
  • Pyr = Abbreviation for the pyranose form if available, “NA” if not
  • Fur = Abbreviation for the furanose form if available, “NA” if not
  • #C (main) = Number of carbons in the main saccharide chain.  That is, although GlcNAc technically contains 7 carbons, it is still a hexose, so the number listed in this column is 6.
  • Ano = Anomeric position (1 for aldoses and typically 2 for ketoses)
  • Name = Unabbreviated common name.
  • Forms and Linkages = linkages available for each available form.
    • The available linkages must pair with the forms available.
    • Forms consist of three letters:
      • First letter: a or b for alpha or beta
      • Second letter: D or L for the D or L form
      • Third letter: p or f for pyranoside or furanoside
      • If a field is omitted, then the specified linkage list applies to both forms.  For example:
          • “ap” means that the list applies to both the D and L forms, but only for the alpha pyranoside.
          • “p” means that the list applies to all variants of alpha, beta, D & L for the pyranoside form.
          • “aLp” means the list applies only to the L enantiomer of the alpha pyranoside.
      • If a form combination is not listed, then that combination is not available at all.
    • Linkage lists refer to all linkage positions and combinations of positions that are available for the indicated form.  
      • See the notes after the table for a legend.  
      • If the anomeric position is listed in the attachments list, then this residue can be specified as the reducing-end-terminal residue for anomeric-anomeric linking.
TLCGCReadyPyrFur#C (main)AnoNameForms and Linkages
AllNYAllpNA61allose
p0,1,2,3,4,6,P,Q,R,S,T,U,V,W,X,Y,Z
AltEYAltpNA61altrose
p0,1,2,3,4,6,P,Q,R,S,T,U,V,W,X,Y,Z
AraAYArapAraf51arabinose
p0,1,2,3,4,T,W,Y,Z
f0,1,2,3,5,Z
FruCYFrupFruf62fructose
p0,1,2,3,4,5,W
f0,1,2,3,4,6,U,V,W
FucFYFucpNA61fucose
p0,1,2,3,4,T,W,Y,Z
GalLYGalpNA61galactose
p0,1,2,3,4,6,P,Q,R,S,T,U,V,W,X,Y,Z
GalAOYGalpANA61galacturonate
p0,1,2,3,4,T,W,Y,Z
GalNAcVYGalpNAcNA61N-acetylgalactosamine
p0,1,3,4,6,Q,U,V,W
GlcGYGlcpNA61glucose
p0,1,2,3,4,6,P,Q,R,S,T,U,V,W,X,Y,Z
GlcAZYGlcpANA61glucuronate
p0,1,2,3,4,T,W,Y,Z
GlcNAcYYGlcpNAcNA61N-acetylglucosamine
p0,1,3,4,6,Q,U,V,W
GulKYGulpNA61gulose
p0,1,2,3,4,6,P,Q,R,S,T,U,V,W,X,Y,Z
IdononeNNANA61idose
IdoAUYIdopANA61iduronate
p0,1,2,3,4,T,W,Y,Z
KDNnoneNNANA922-keto-3-deoxy-nonulosonate
KDOnoneNNANA822-keto-3-deoxy-octulosonate
LyxDYLyxpLyxf51lyxose
p0,1,2,3,4,T,W,Y,Z
f0,1,2,3,5,Z
ManMYManpNA61mannose
p0,1,2,3,4,6,P,Q,R,S,T,U,V,W,X,Y,Z
ManNAcWYManpNAcNA61N-acetylmannosamine
p0,1,3,4,6,Q,U,V,W
Neu5AcSAYNeup5AcNA925-N-acetylneuraminate
ap0,4,7,8,9,A,B,C,D,E,F,G,H,I,J,K
Neu5GcGLYNeup5GcNA925-N-glycolylneuraminate
ap0,4,7,8,9,A,B,C,D,E,F,G,H,I,J,K
PsiPYPsipPsif62psicose
p0,1,2,3,4,5,W
f0,1,2,3,4,6,U,V,W
QuiQYQuipNA61quinovose
p0,1,2,3,4,T,W,Y,Z
RhaHYRhapNA61rhamnose
p0,1,2,3,4,T,W,Y,Z
RibRYRibpRibf51ribose
p0,1,2,3,4,T,W,Y,Z
f0,1,2,3,5,Z
SorBYSorpSorf62sorbose
p0,1,2,3,4,5,W
f0,1,2,3,4,6,U,V,W
TagJYTagpTagf62tagatose
p0,1,2,3,4,5,W
f0,1,2,3,4,6,Q,U,V,W
TalTYTalpNA61talose
p0,1,2,3,4,6,P,Q,R,S,T,U,V,W,X,Y,Z
XylXYXylpXylf51xylose
p0,1,2,3,4,T,W,Y,Z
f0,1,2,3,5,Z

Key to attachment locations:

All codes below, except as noted, indicate an open valence at the anomeric carbon.  That is, all except those noted possess the linkage capability in the “0” (zero) residue.

Numbers:

  • 0 (zero):  The residue has open valence only at the anomeric carbon. It can be used only to terminate the non-reducing end of a chain.
  • 1 (one) might mean:
    • If 1 is NOT the anomeric position: The residue has open valence at the anomeric carbon and at O1 (oxygen 1).
    • If 1 IS the anomeric position: The residue has open valence ONLY at O1 (oxygen 1).
  • 2 (two) might mean:
    • If 2 is NOT the anomeric position:  The residue has open valence at the anomeric carbon and at O2 (oxygen 2). 
    • If 2 IS the anomeric position:  The residue has open valence ONLY at O2 (oxygen 2).
  • 3 – 9 (three through nine):
    • The residue has an open valence at its anomeric carbon and at the oxygen corresponding to the number.

Letters:

Letters correspond to residues with multiple linkage points. The oxygens that have open valences are listed.  All letters also imply an open valence at the anomeric carbon.

  • A:  9,8,7,4
  • B:  9,8,7
  • C:  9,8,4
  • D:  9,7,4
  • E:  8,7,4
  • F:  9,8
  • G:  9,7
  • H:  8,7
  • I:  9,4
  • J:  8,4
  • K:  7,4
  • P:  2,3,4,6
  • Q:  3,4,6
  • R:  2,4,6
  • S:  2,3,6
  • T:  2,3,4
  • U:  4,6
  • V:  3,6
  • W:  3,4
  • X:  2,6
  • Y:  2,4
  • Z:  2,3

 

Table 2: aglycons

See the glycans table notes for a description of the table columns except for
“Formula”, the meaning of which is pretty obvious.

================================================================================
TLC GC Ready Formula Name
================================================================================
@BEGIN_AGLYCONS
OH ROH Y -OH hydroxyl
OME OME Y -OCH3 O-methyl
OTBU TBT Y -OCH(CH3)2 O-tert-butyl
@END_AGLYCONS
================================================================================

================================================================================
Table 3: GLYCAM synonyms table
================================================================================

The table below provides common synonyms for some of the “TLC” codes in the
tables above.

================================================================================
Recommended
“TLC” List of synonyms
================================================================================
@BEGIN_SYNONYMS
Neu5Ac NeuNAc
@END_SYNONYMS
================================================================================

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