Hmdb loader
Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2022-11-30 19:02:44 UTC
HMDB IDHMDB0004846
Secondary Accession Numbers
  • HMDB04846
Metabolite Identification
Common NameGanglioside GM3 (d18:1/20:0)
DescriptionGanglioside GM3 (d18:1/20:0) is a glycosphingolipid (ceramide and oligosaccharide)or oligoglycosylceramide with one or more sialic acids (i.e. n-acetylneuraminic acid) linked on the sugar chain. It is a component the cell plasma membrane which modulates cell signal transduction events. Gangliosides have been found to be highly important in immunology. Ganglioside GM3 carries a net-negative charge at pH 7.0 and is acidic. Gangliosides can amount to 6% of the weight of lipids from brain, but they are found at low levels in all animal tissuesGangliosides are glycosphingolipids. There are four types of glycosphingolipids, the cerebrosides, sulfatides, globosides and gangliosides. Gangliosides are very similar to globosides except that they also contain N-acetyl neuraminic acid (NANA) in varying amounts. The specific names for the gangliosides provide information about their structure. The letter G refers to ganglioside, and the subscripts M, D, T and Q indicate that the molecule contains mono-, di-, tri and quatra-sialic acid. The numbered subscripts 1, 2 and 3 refer to the carbohydrate sequence that is attached to the ceramide. In particular, 1 stands for GalGalNAcGalGlc-ceramide, 2 stands for GalNAcGalGlc-ceramide and 3 stands for GalGlc-ceramide. Deficiencies in lysosomal enzymes that degrade the carbohydrate portions of various gangliosides are responsible for a number of lysosomal storage diseases such as Tay-Sachs disease, Sandhoff disease, and GM1 gangliosidosis. The carbohydrate portion of the ganglioside GM1 is the site of attachment of cholera toxin, the protein secreted by Vibrio cholerae.
Structure
Data?1582752318
Synonyms
ValueSource
(N-Acetylneuraminyl)-D-galactosyl-D-glucosylceramideHMDB
(N-Acetylneuraminyl)-delta-galactosyl-delta-glucosylceramideHMDB
alpha-N-Acetylneuraminyl-2,3-beta-D-galactosyl-1,4-beta-D-glucosylceramideHMDB
alpha-N-Acetylneuraminyl-2,3-beta-delta-galactosyl-1,4-beta-delta-glucosylceramideHMDB
Ganglioside GM3HMDB
Ganglioside m3HMDB
GLac1HMDB
GM3HMDB
HematosideHMDB
N-Acetylneuraminyl-2,3-alpha-D-galactosyl-1,4-beta-D-glucosylceramideHMDB
N-Acetylneuraminyl-2,3-alpha-delta-galactosyl-1,4-beta-delta-glucosylceramideHMDB
Neu5ac-alpha2->3gal-beta1->4GLC-beta1->1'cerHMDB
SialosyllactosylceramideHMDB
(2S,4S,5R)-2-{[(2S,3R,4S,5S,6R)-2-{[(2R,3S,4R,6R)-4,5-dihydroxy-6-{[(2S,3R)-3-hydroxy-2-[(1-hydroxyicosylidene)amino]octadec-4-en-1-yl]oxy}-2-(hydroxymethyl)oxan-3-yl]oxy}-3,5-dihydroxy-6-(hydroxymethyl)oxan-4-yl]oxy}-4-hydroxy-5-[(1-hydroxyethylidene)amino]-6-[(1R,2R)-1,2,3-trihydroxypropyl]oxane-2-carboxylateHMDB
Chemical FormulaC61H112N2O21
Average Molecular Weight1209.5428
Monoisotopic Molecular Weight1208.775758656
IUPAC Name(2S,4S,5R)-2-{[(2S,3R,4S,5S,6R)-2-{[(2R,3S,4R,6R)-4,5-dihydroxy-6-{[(2S,3R,4E)-3-hydroxy-2-icosanamidooctadec-4-en-1-yl]oxy}-2-(hydroxymethyl)oxan-3-yl]oxy}-3,5-dihydroxy-6-(hydroxymethyl)oxan-4-yl]oxy}-5-acetamido-4-hydroxy-6-[(1R,2R)-1,2,3-trihydroxypropyl]oxane-2-carboxylic acid
Traditional Name(2S,4S,5R)-2-{[(2S,3R,4S,5S,6R)-2-{[(2R,3S,4R,6R)-4,5-dihydroxy-6-{[(2S,3R,4E)-3-hydroxy-2-icosanamidooctadec-4-en-1-yl]oxy}-2-(hydroxymethyl)oxan-3-yl]oxy}-3,5-dihydroxy-6-(hydroxymethyl)oxan-4-yl]oxy}-5-acetamido-4-hydroxy-6-[(1R,2R)-1,2,3-trihydroxypropyl]oxane-2-carboxylic acid
CAS Registry NumberNot Available
SMILES
CCCCCCCCCCCCCCCCCCCC(=O)N[C@@H](CO[C@@H]1O[C@H](CO)[C@@H](O[C@@H]2O[C@H](CO)[C@H](O)[C@H](O[C@@]3(C[C@H](O)[C@@H](NC(C)=O)C(O3)[C@H](O)[C@H](O)CO)C(O)=O)[C@H]2O)[C@H](O)C1O)[C@H](O)\C=C\CCCCCCCCCCCCC
InChI Identifier
InChI=1S/C61H112N2O21/c1-4-6-8-10-12-14-16-18-19-20-21-23-25-27-29-31-33-35-48(71)63-42(43(68)34-32-30-28-26-24-22-17-15-13-11-9-7-5-2)40-79-58-53(75)52(74)55(47(39-66)81-58)82-59-54(76)57(51(73)46(38-65)80-59)84-61(60(77)78)36-44(69)49(62-41(3)67)56(83-61)50(72)45(70)37-64/h32,34,42-47,49-59,64-66,68-70,72-76H,4-31,33,35-40H2,1-3H3,(H,62,67)(H,63,71)(H,77,78)/b34-32+/t42-,43+,44-,45+,46+,47+,49+,50+,51-,52+,53?,54+,55+,56?,57-,58+,59-,61-/m0/s1
InChI KeySIJZEDYROBAHFV-DSRQLKEMSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as gangliosides. These are lipid molecules composed of a glycosphingolipid (ceramide and saccharide) with one or more sialic acids linked on the sugar chain. They are usually oligoglycosylceramides derived from lactosylceramide and containing a sialic acid residue such as N-acetylneuraminic acid.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassSphingolipids
Sub ClassGlycosphingolipids
Direct ParentGangliosides
Alternative Parents
Substituents
  • Neuaca2-3galb1-4glcb-cer_backbone
  • Glycosyl-n-acylsphingosine
  • Oligosaccharide
  • N-acylneuraminic acid or derivatives
  • N-acylneuraminic acid
  • Neuraminic acid
  • Fatty acyl glycoside
  • C-glucuronide
  • Alkyl glycoside
  • C-glycosyl compound
  • Glycosyl compound
  • O-glycosyl compound
  • Ketal
  • Fatty amide
  • N-acyl-amine
  • Fatty acyl
  • Oxane
  • Pyran
  • Acetamide
  • Secondary carboxylic acid amide
  • Secondary alcohol
  • Carboxamide group
  • Polyol
  • Carboxylic acid derivative
  • Carboxylic acid
  • Acetal
  • Oxacycle
  • Monocarboxylic acid or derivatives
  • Organoheterocyclic compound
  • Organic oxide
  • Organic oxygen compound
  • Organooxygen compound
  • Organonitrogen compound
  • Primary alcohol
  • Hydrocarbon derivative
  • Organic nitrogen compound
  • Organopnictogen compound
  • Alcohol
  • Carbonyl group
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
ProcessNot Available
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water Solubility0Not Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility0.02 g/LALOGPS
logP4.37ALOGPS
logP6.7ChemAxon
logS-4.8ALOGPS
pKa (Strongest Acidic)2.84ChemAxon
pKa (Strongest Basic)-3.6ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count21ChemAxon
Hydrogen Donor Count14ChemAxon
Polar Surface Area373.41 ŲChemAxon
Rotatable Bond Count47ChemAxon
Refractivity309.28 m³·mol⁻¹ChemAxon
Polarizability139.68 ųChemAxon
Number of Rings3ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+329.43630932474
DeepCCS[M-H]-327.78330932474
DeepCCS[M-2H]-361.81630932474
DeepCCS[M+Na]+335.59330932474

Predicted Kovats Retention Indices

Not Available
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ganglioside GM3 (d18:1/20:0) 10V, Negative-QTOFsplash10-0a4r-6190000100-46782cac9ef9afc21ead2021-09-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ganglioside GM3 (d18:1/20:0) 20V, Negative-QTOFsplash10-0a59-3490300100-c2dbbeedbb6f8e68caba2021-09-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ganglioside GM3 (d18:1/20:0) 40V, Negative-QTOFsplash10-052o-7362091301-eacab3109f04f31c7e942021-09-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ganglioside GM3 (d18:1/20:0) 10V, Positive-QTOFsplash10-0a4l-3770790201-858c7bfaf62881fcb2242021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ganglioside GM3 (d18:1/20:0) 20V, Positive-QTOFsplash10-0pki-3431940700-5c060ab3081d40addf292021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ganglioside GM3 (d18:1/20:0) 40V, Positive-QTOFsplash10-053s-9150330000-a0d35b616c8f8f03b1d22021-09-25Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Extracellular
  • Membrane
Biospecimen LocationsNot Available
Tissue Locations
  • Adrenal Gland
  • Brain
  • Epidermis
  • Fibroblasts
  • Neuron
  • Testis
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB023447
KNApSAcK IDNot Available
Chemspider ID16744863
KEGG Compound IDC04730
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN ID7105
PubChem Compound20057287
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Ishii A, Ohta M, Watanabe Y, Matsuda K, Ishiyama K, Sakoe K, Nakamura M, Inokuchi J, Sanai Y, Saito M: Expression cloning and functional characterization of human cDNA for ganglioside GM3 synthase. J Biol Chem. 1998 Nov 27;273(48):31652-5. [PubMed:9822625 ]
  2. Caudie C, Vial C, Petiot P, Bancel J, Lombard C, Gonnaud PM: [Monoclonal IgM autoantibody activity vis-a-vis glycoconjugates of peripheral nerves: apropos of 112 cases]. Ann Biol Clin (Paris). 2001 Sep-Oct;59(5):567-77. [PubMed:11602387 ]
  3. Toledo MS, Suzuki E, Handa K, Hakomori S: Effect of ganglioside and tetraspanins in microdomains on interaction of integrins with fibroblast growth factor receptor. J Biol Chem. 2005 Apr 22;280(16):16227-34. Epub 2005 Feb 14. [PubMed:15710618 ]
  4. Valaperta R, Chigorno V, Basso L, Prinetti A, Bresciani R, Preti A, Miyagi T, Sonnino S: Plasma membrane production of ceramide from ganglioside GM3 in human fibroblasts. FASEB J. 2006 Jun;20(8):1227-9. Epub 2006 Apr 27. [PubMed:16645048 ]
  5. Paller AS, Siegel JN, Spalding DE, Bremer EG: Absence of a stratum corneum antigen in disorders of epidermal cell proliferation: detection with an anti-ganglioside GM3 antibody. J Invest Dermatol. 1989 Feb;92(2):240-6. [PubMed:2645370 ]
  6. Dawson G: Glycosphingolipid levels in an unusual neurovisceral storage disease characterized by lactosylceramide galactosyl hydrolase deficiency: lactosylceramidosis. J Lipid Res. 1972 Mar;13(2):207-19. [PubMed:5016302 ]
  7. Schriever F, Dennis RD, Pallmann B, Riethmuller G, Johnson JP: Monoclonal antibody MACG1 distinguishes between different molecular species of the ganglioside GM3. Hybridoma. 1989 Apr;8(2):153-9. [PubMed:2714813 ]

Only showing the first 10 proteins. There are 48 proteins in total.

Enzymes

General function:
Involved in exo-alpha-sialidase activity
Specific function:
Hydrolyzes sialylated compounds.
Gene Name:
NEU2
Uniprot ID:
Q9Y3R4
Molecular weight:
Not Available
General function:
Involved in exo-alpha-sialidase activity
Specific function:
May function in lysosomal catabolism of sialylated glycoconjugates. Has sialidase activity towards synthetic substrates, such as 2'-(4-methylumbelliferyl)-alpha-D-N-acetylneuraminic acid (4-MU-NANA or 4MU-NeuAc). Has a broad substrate specificity being active on glycoproteins, oligosaccharides and sialylated glycolipids.
Gene Name:
NEU4
Uniprot ID:
Q8WWR8
Molecular weight:
Not Available
General function:
Involved in transferase activity, transferring hexosyl groups
Specific function:
Catalyzes the formation of some glycolipid via the addition of N-acetylgalactosamine (GalNAc) in alpha-1,3-linkage to some substrate. Glycolipids probably serve for adherence of some pathogens
Gene Name:
GBGT1
Uniprot ID:
Q8N5D6
Molecular weight:
40126.9
General function:
Involved in N-acetylglucosaminylphosphatidylinositol de
Specific function:
Involved in the second step of GPI biosynthesis. De-N-acetylation of N-acetylglucosaminyl-phosphatidylinositol.
Gene Name:
PIGL
Uniprot ID:
Q9Y2B2
Molecular weight:
28530.965
General function:
Involved in sialyltransferase activity
Specific function:
Catalyzes the formation of ganglioside GM3 (alpha-N-acetylneuraminyl-2,3-beta-D-galactosyl-1, 4-beta-D-glucosylceramide).
Gene Name:
ST3GAL5
Uniprot ID:
Q9UNP4
Molecular weight:
45584.69
General function:
Involved in beta-N-acetylhexosaminidase activity
Specific function:
Responsible for the degradation of GM2 gangliosides, and a variety of other molecules containing terminal N-acetyl hexosamines, in the brain and other tissues.
Gene Name:
HEXB
Uniprot ID:
P07686
Molecular weight:
Not Available
General function:
Involved in beta-N-acetylhexosaminidase activity
Specific function:
Responsible for the degradation of GM2 gangliosides, and a variety of other molecules containing terminal N-acetyl hexosamines, in the brain and other tissues. The form B is active against certain oligosaccharides. The form S has no measurable activity.
Gene Name:
HEXA
Uniprot ID:
P06865
Molecular weight:
Not Available
General function:
Involved in transferase activity, transferring hexosyl groups
Specific function:
Involved in the biosynthesis of gangliosides GM2, GD2 and GA2.
Gene Name:
B4GALNT1
Uniprot ID:
Q00973
Molecular weight:
58881.78
General function:
Involved in phosphatidylinositol N-acetylglucosaminyltransferase activity
Specific function:
Part of the complex catalyzing the transfer of N-acetylglucosamine from UDP-N-acetylglucosamine to phosphatidylinositol, the first step of GPI biosynthesis.
Gene Name:
PIGQ
Uniprot ID:
Q9BRB3
Molecular weight:
65343.25
General function:
Involved in biosynthetic process
Specific function:
Necessary for the synthesis of N-acetylglucosaminyl-phosphatidylinositol, the very early intermediate in GPI-anchor biosynthesis.
Gene Name:
PIGA
Uniprot ID:
P37287
Molecular weight:
54126.065

Only showing the first 10 proteins. There are 48 proteins in total.