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(2S,4S,5R,6R)-2,4-Dihydroxy-5-(2-hydroxyacetamido)-6-((1R,2R)-1,2,3-trihydroxypropyl)tetrahydro-2H-pyran-2-carboxylic acid

PubChem CID
123802
Structure
(2S,4S,5R,6R)-2,4-Dihydroxy-5-(2-hydroxyacetamido)-6-((1R,2R)-1,2,3-trihydroxypropyl)tetrahydro-2H-pyran-2-carboxylic acid_small.png
(2S,4S,5R,6R)-2,4-Dihydroxy-5-(2-hydroxyacetamido)-6-((1R,2R)-1,2,3-trihydroxypropyl)tetrahydro-2H-pyran-2-carboxylic acid_3D_Structure.png
Molecular Formula
Synonyms
  • GcNeu
  • 1113-83-3
  • NeuGc
  • NGNA
  • N-glycolyl-beta-neuraminic acid
Molecular Weight
325.27 g/mol
Computed by PubChem 2.2 (PubChem release 2021.10.14)
Dates
  • Create:
    2005-08-08
  • Modify:
    2024-12-07
Description
N-glycoloyl-beta-neuraminic acid is an N-acylneuraminic acid in which the acyl substituent on nitrogen is glycolyl and which has beta-configuration at the anomeric centre. It has a role as a mammalian metabolite and an antigen.
GcNeu has been reported in Ambystoma mexicanum with data available.
See also: N-Glycolyl-Neuraminic acid (annotation moved to).

1 Structures

1.1 2D Structure

Chemical Structure Depiction
(2S,4S,5R,6R)-2,4-Dihydroxy-5-(2-hydroxyacetamido)-6-((1R,2R)-1,2,3-trihydroxypropyl)tetrahydro-2H-pyran-2-carboxylic acid.png

1.2 3D Conformer

2 Biologic Description

1 of 2
SVG Image
SVG Image
IUPAC Condensed
b-NeuGc
LINUCS
[][b-NeupGc]{}
IUPAC
3,5-dideoxy-5-glycolamido-D-glycero-beta-D-galacto-non-2-ulopyranosonic acid
2 of 2
Permethylated Mass
Monosaccharide Composition

3 Names and Identifiers

3.1 Computed Descriptors

3.1.1 IUPAC Name

(2S,4S,5R,6R)-2,4-dihydroxy-5-[(2-hydroxyacetyl)amino]-6-[(1R,2R)-1,2,3-trihydroxypropyl]oxane-2-carboxylic acid
Computed by Lexichem TK 2.7.0 (PubChem release 2021.10.14)

3.1.2 InChI

InChI=1S/C11H19NO10/c13-2-5(16)8(18)9-7(12-6(17)3-14)4(15)1-11(21,22-9)10(19)20/h4-5,7-9,13-16,18,21H,1-3H2,(H,12,17)(H,19,20)/t4-,5+,7+,8+,9+,11-/m0/s1
Computed by InChI 1.0.6 (PubChem release 2021.10.14)

3.1.3 InChIKey

FDJKUWYYUZCUJX-AJKRCSPLSA-N
Computed by InChI 1.0.6 (PubChem release 2021.10.14)

3.1.4 SMILES

C1[C@@H]([C@H]([C@@H](O[C@@]1(C(=O)O)O)[C@@H]([C@@H](CO)O)O)NC(=O)CO)O
Computed by OEChem 2.3.0 (PubChem release 2021.10.14)

3.2 Molecular Formula

C11H19NO10
Computed by PubChem 2.2 (PubChem release 2021.10.14)

3.3 Other Identifiers

3.3.1 CAS

1113-83-3

3.3.2 ChEBI ID

3.3.3 ChEMBL ID

3.3.4 HMDB ID

3.3.5 Nikkaji Number

3.3.6 Wikidata

3.4 Synonyms

3.4.1 MeSH Entry Terms

  • GcNeu
  • N-glycoloylneuraminic acid
  • N-glycolylneuraminic acid
  • N-glycolylneuraminic acid, (alpha-D-Gal)-isomer
  • NGNA

3.4.2 Depositor-Supplied Synonyms

4 Chemical and Physical Properties

4.1 Computed Properties

Property Name
Molecular Weight
Property Value
325.27 g/mol
Reference
Computed by PubChem 2.2 (PubChem release 2021.10.14)
Property Name
XLogP3-AA
Property Value
-4.1
Reference
Computed by XLogP3 3.0 (PubChem release 2021.10.14)
Property Name
Hydrogen Bond Donor Count
Property Value
8
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.10.14)
Property Name
Hydrogen Bond Acceptor Count
Property Value
10
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.10.14)
Property Name
Rotatable Bond Count
Property Value
6
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.10.14)
Property Name
Exact Mass
Property Value
325.10089580 Da
Reference
Computed by PubChem 2.2 (PubChem release 2021.10.14)
Property Name
Monoisotopic Mass
Property Value
325.10089580 Da
Reference
Computed by PubChem 2.2 (PubChem release 2021.10.14)
Property Name
Topological Polar Surface Area
Property Value
197Ų
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.10.14)
Property Name
Heavy Atom Count
Property Value
22
Reference
Computed by PubChem
Property Name
Formal Charge
Property Value
0
Reference
Computed by PubChem
Property Name
Complexity
Property Value
418
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.10.14)
Property Name
Isotope Atom Count
Property Value
0
Reference
Computed by PubChem
Property Name
Defined Atom Stereocenter Count
Property Value
6
Reference
Computed by PubChem
Property Name
Undefined Atom Stereocenter Count
Property Value
0
Reference
Computed by PubChem
Property Name
Defined Bond Stereocenter Count
Property Value
0
Reference
Computed by PubChem
Property Name
Undefined Bond Stereocenter Count
Property Value
0
Reference
Computed by PubChem
Property Name
Covalently-Bonded Unit Count
Property Value
1
Reference
Computed by PubChem
Property Name
Compound Is Canonicalized
Property Value
Yes
Reference
Computed by PubChem (release 2021.10.14)

4.2 Experimental Properties

4.2.1 Physical Description

Solid

5 Spectral Information

5.1 Mass Spectrometry

5.1.1 GC-MS

1 of 4
View All
Spectra ID
Instrument Type
GC-MS
Top 5 Peaks

103.0 1

217.0 0.66

334.0 0.49

133.0 0.45

117.0 0.38

Thumbnail
Thumbnail
2 of 4
View All
Spectra ID
Instrument Type
GC-MS
Top 5 Peaks

103.0 1

217.0 0.48

133.0 0.41

117.0 0.39

334.0 0.32

Thumbnail
Thumbnail

5.1.2 MS-MS

1 of 7
View All
Spectra ID
Instrument Type
LC-ESI-QQ
Ionization Mode
negative
Top 5 Peaks

324.5 100

236.0 6.06

116.2 1.48

186.1 0.77

306.7 0.52

Thumbnail
Thumbnail
Notes
instrument=API3000, Applied Biosystems
2 of 7
View All
Spectra ID
Instrument Type
LC-ESI-QQ
Ionization Mode
negative
Top 5 Peaks

116.0 100

186.2 35.34

87.1 25.64

236.2 24.20

324.6 15.18

Thumbnail
Thumbnail
Notes
instrument=API3000, Applied Biosystems

5.1.3 LC-MS

1 of 3
View All
MoNA ID
MS Category
Experimental
MS Type
LC-MS
MS Level
MS2
Precursor Type
[M+H]+
Precursor m/z
326
Instrument
API3000, Applied Biosystems
Instrument Type
LC-ESI-QQ
Ionization Mode
positive
Collision Energy
50 V
Top 5 Peaks

83.000 100

67.000 50

105.300 44.74

100.000 44.74

55.100 39.47

Thumbnail
Thumbnail
License
CC BY-NC-SA
2 of 3
View All
MoNA ID
MS Category
Experimental
MS Type
LC-MS
MS Level
MS2
Precursor Type
[M+H]+
Precursor m/z
326
Instrument
API3000, Applied Biosystems
Instrument Type
LC-ESI-QQ
Ionization Mode
positive
Collision Energy
40 V
Top 5 Peaks

100.000 100

83.300 82.19

105.100 54.79

59.100 41.10

120.900 39.73

Thumbnail
Thumbnail
License
CC BY-NC-SA

7 Chemical Vendors

8 Pharmacology and Biochemistry

8.1 Human Metabolite Information

8.1.1 Tissue Locations

Spleen

8.1.2 Cellular Locations

Cytoplasm

9 Literature

9.1 Consolidated References

9.2 NLM Curated PubMed Citations

9.3 Springer Nature References

9.4 Chemical Co-Occurrences in Literature

9.5 Chemical-Gene Co-Occurrences in Literature

9.6 Chemical-Disease Co-Occurrences in Literature

10 Patents

10.1 Depositor-Supplied Patent Identifiers

10.2 WIPO PATENTSCOPE

10.3 Chemical Co-Occurrences in Patents

10.4 Chemical-Disease Co-Occurrences in Patents

10.5 Chemical-Gene Co-Occurrences in Patents

11 Interactions and Pathways

11.1 Protein Bound 3D Structures

11.1.1 Ligands from Protein Bound 3D Structures

PDBe Ligand Code
PDBe Structure Code
PDBe Conformer

12 Biological Test Results

12.1 BioAssay Results

13 Taxonomy

The LOTUS Initiative for Open Natural Products Research: frozen dataset union wikidata (with metadata) | DOI:10.5281/zenodo.5794106

14 Classification

14.1 MeSH Tree

14.2 ChEBI Ontology

14.3 ChemIDplus

14.4 LOTUS Tree

14.5 Glycan Naming and Subsumption Ontology (GNOme)

14.6 MolGenie Organic Chemistry Ontology

15 Information Sources

  1. ChEBI
  2. LOTUS - the natural products occurrence database
    LICENSE
    The code for LOTUS is released under the GNU General Public License v3.0.
    https://lotus.nprod.net/
  3. ChEMBL
    LICENSE
    Access to the web interface of ChEMBL is made under the EBI's Terms of Use (http://www.ebi.ac.uk/Information/termsofuse.html). The ChEMBL data is made available on a Creative Commons Attribution-Share Alike 3.0 Unported License (http://creativecommons.org/licenses/by-sa/3.0/).
    http://www.ebi.ac.uk/Information/termsofuse.html
  4. ChemIDplus
    ChemIDplus Chemical Information Classification
    https://pubchem.ncbi.nlm.nih.gov/source/ChemIDplus
  5. Human Metabolome Database (HMDB)
    LICENSE
    HMDB is offered to the public as a freely available resource. Use and re-distribution of the data, in whole or in part, for commercial purposes requires explicit permission of the authors and explicit acknowledgment of the source material (HMDB) and the original publication (see the HMDB citing page). We ask that users who download significant portions of the database cite the HMDB paper in any resulting publications.
    http://www.hmdb.ca/citing
  6. GlyGen
  7. MassBank of North America (MoNA)
    LICENSE
    The content of the MoNA database is licensed under CC BY 4.0.
    https://mona.fiehnlab.ucdavis.edu/documentation/license
  8. NIST Mass Spectrometry Data Center
    LICENSE
    Data covered by the Standard Reference Data Act of 1968 as amended.
    https://www.nist.gov/srd/public-law
    N-Glycolylneuraminic acid
    http://www.nist.gov/srd/nist1a.cfm
  9. Japan Chemical Substance Dictionary (Nikkaji)
  10. Protein Data Bank in Europe (PDBe)
  11. RCSB Protein Data Bank (RCSB PDB)
    LICENSE
    Data files contained in the PDB archive (ftp://ftp.wwpdb.org) are free of all copyright restrictions and made fully and freely available for both non-commercial and commercial use. Users of the data should attribute the original authors of that structural data.
    https://www.rcsb.org/pages/policies
  12. Springer Nature
  13. Wikidata
    N-glycoloyl-beta-neuraminic acid
    https://www.wikidata.org/wiki/Q309533
  14. PubChem
  15. Medical Subject Headings (MeSH)
    LICENSE
    Works produced by the U.S. government are not subject to copyright protection in the United States. Any such works found on National Library of Medicine (NLM) Web sites may be freely used or reproduced without permission in the U.S.
    https://www.nlm.nih.gov/copyright.html
  16. Glycan Naming and Subsumption Ontology (GNOme)
    GNOme
  17. MolGenie
    MolGenie Organic Chemistry Ontology
    https://github.com/MolGenie/ontology/
  18. PATENTSCOPE (WIPO)
CONTENTS