Showing metabocard for Ganglioside GM2 (d18:1/9Z-18:1) (BMDB0004937)

IdentificationTaxonomyPhysical propertiesPathwaysSpectraConcentrationsLinksReferencesXML
Record Information
Version1.0
Creation Date2016-09-30 23:13:18 UTC
Update Date2020-05-11 20:32:08 UTC
BMDB IDBMDB0004937
Secondary Accession Numbers
  • BMDB04937
Metabolite Identification
Common NameGanglioside GM2 (d18:1/9Z-18:1)
DescriptionGanglioside GM2 (d18:1/9Z-18:1), also known as ganglioside GM2 or ii3neuacggose3cer, belongs to the class of organic compounds known as galnacb1-4galb1-4glc- (ganglio series). These are neutral glycosphingolipids in which the root sequence is GalNAcb1-4Galb1-4Glc. Ganglioside GM2 (d18:1/9Z-18:1) is an extremely weak basic (essentially neutral) compound (based on its pKa).
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
ValueSource
(2S,5S,6S)-2-{[(2R,3S,4R,5R,6S)-3-{[(2S,3R,4R,5R,6R)-4,5-dihydroxy-3-[(1-hydroxyethylidene)amino]-6-(hydroxymethyl)oxan-2-yl]oxy}-6-{[(2R,3S,4R,5R,6R)-4,5-dihydroxy-6-{[(2S,3R,4E)-3-hydroxy-2-{[(9Z)-1-hydroxyoctadec-9-en-1-ylidene]amino}octadec-4-en-1-yl]oxy}-2-(hydroxymethyl)oxan-3-yl]oxy}-5-hydroxy-2-(hydroxymethyl)oxan-4-yl]oxy}-6-hydroxy-5-[(1-hydroxyethylidene)amino]-4-[(1S,2R)-1,2,3-trihydroxypropyl]oxane-2-carboxylateHMDB
GalNAc-beta1->4(neu5ac-alpha2->3)gal-beta1->4GLC-beta1->1'cerHMDB
Ganglioside GM2HMDB
GM2HMDB
II3neuacggose3cerHMDB
N-Acetyl-D-galactosaminyl-(N-acetylneuraminyl)-D-galactosyl-1,4-beta-D-glucosyl-N-acylsphingosineHMDB
N-Acetyl-D-galactosaminyl-(N-acetylneuraminyl)-D-galactosyl-D-glucosylceramideHMDB
N-Acetyl-delta-galactosaminyl-(N-acetylneuraminyl)-delta-galactosyl-1,4-beta-delta-glucosyl-N-acylsphingosineHMDB
N-Acetyl-delta-galactosaminyl-(N-acetylneuraminyl)-delta-galactosyl-delta-glucosylceramideHMDB
N-Acetyl-ganglioside GM2HMDB
N-Acetylganglioside GM2HMDB
NeuAc-GM2HMDB
Tay-sachs gangliosideHMDB
Chemical FormulaC67H119N3O26
Average Molecular Weight1382.6663
Monoisotopic Molecular Weight1381.808180995
IUPAC Name(2S,5S,6S)-2-{[(2S,3R,4R,5S,6R)-2-{[(2R,3S,4R,5R,6R)-4,5-dihydroxy-6-{[(2S,3R,4E)-3-hydroxy-2-[(9Z)-octadec-9-enamido]octadec-4-en-1-yl]oxy}-2-(hydroxymethyl)oxan-3-yl]oxy}-5-{[(2S,3R,4R,5R,6R)-3-acetamido-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3-hydroxy-6-(hydroxymethyl)oxan-4-yl]oxy}-5-acetamido-6-hydroxy-4-[(1S,2R)-1,2,3-trihydroxypropyl]oxane-2-carboxylic acid
Traditional Name(2S,5S,6S)-2-{[(2S,3R,4R,5S,6R)-2-{[(2R,3S,4R,5R,6R)-4,5-dihydroxy-6-{[(2S,3R,4E)-3-hydroxy-2-[(9Z)-octadec-9-enamido]octadec-4-en-1-yl]oxy}-2-(hydroxymethyl)oxan-3-yl]oxy}-5-{[(2S,3R,4R,5R,6R)-3-acetamido-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3-hydroxy-6-(hydroxymethyl)oxan-4-yl]oxy}-5-acetamido-6-hydroxy-4-[(1S,2R)-1,2,3-trihydroxypropyl]oxane-2-carboxylic acid
CAS Registry NumberNot Available
SMILES
CCCCCCCCCCCCC\C=C\[C@@H](O)[C@H](CO[C@@H]1O[C@H](CO)[C@@H](O[C@@H]2O[C@H](CO)[C@H](O[C@@H]3O[C@H](CO)[C@H](O)[C@H](O)[C@H]3NC(C)=O)[C@H](O[C@]3(CC([C@H](O)[C@H](O)CO)[C@H](NC(C)=O)[C@@H](O)O3)C(O)=O)[C@H]2O)[C@H](O)[C@H]1O)NC(=O)CCCCCCC\C=C/CCCCCCCC
InChI Identifier
InChI=1S/C67H119N3O26/c1-5-7-9-11-13-15-17-19-20-22-24-26-28-30-32-34-50(79)70-44(45(77)33-31-29-27-25-23-21-18-16-14-12-10-8-6-2)40-89-64-57(84)56(83)59(48(38-73)91-64)93-65-58(85)61(60(49(39-74)92-65)94-63-52(69-42(4)76)55(82)54(81)47(37-72)90-63)95-67(66(87)88)35-43(53(80)46(78)36-71)51(62(86)96-67)68-41(3)75/h19-20,31,33,43-49,51-65,71-74,77-78,80-86H,5-18,21-30,32,34-40H2,1-4H3,(H,68,75)(H,69,76)(H,70,79)(H,87,88)/b20-19-,33-31+/t43?,44-,45+,46+,47+,48+,49+,51-,52+,53-,54-,55+,56+,57+,58+,59+,60-,61+,62-,63-,64+,65-,67-/m0/s1
InChI KeyNHBOQDRLDGHTFT-SIWVGYHTSA-N
Chemical Taxonomy
Description belongs to the class of organic compounds known as galnacb1-4galb1-4glc- (ganglio series). These are neutral glycosphingolipids in which the root sequence is GalNAcb1-4Galb1-4Glc.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassSphingolipids
Sub ClassGlycosphingolipids
Direct ParentGalNAcb1-4Galb1-4Glc- (Ganglio series)
Alternative Parents
Substituents
  • Galnacb1-4galb1-4glcb-cer_backbone
  • Glycosyl-n-acylsphingosine
  • Oligosaccharide
  • Fatty acyl glycoside
  • N-acyl-alpha-hexosamine
  • Alkyl glycoside
  • Glycosyl compound
  • O-glycosyl compound
  • Ketal
  • Fatty amide
  • N-acyl-amine
  • Fatty acyl
  • Oxane
  • Pyran
  • Acetamide
  • Secondary alcohol
  • Carboxamide group
  • Hemiacetal
  • Secondary carboxylic acid amide
  • Polyol
  • Organoheterocyclic compound
  • Acetal
  • Oxacycle
  • Carboxylic acid derivative
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Primary alcohol
  • Organic oxide
  • Organopnictogen compound
  • Organic oxygen compound
  • Hydrocarbon derivative
  • Alcohol
  • Carbonyl group
  • Organooxygen compound
  • Organic nitrogen compound
  • Organonitrogen compound
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
StatusExpected but not Quantified
Origin
  • Endogenous
  • Exogenous
BiofunctionNot Available
ApplicationNot Available
Cellular locations
  • Cell membrane
  • Endosome
  • Membrane
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityInsolubleNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP2.93ALOGPS
logP3.33ChemAxon
logS-4.3ALOGPS
pKa (Strongest Acidic)2.8ChemAxon
pKa (Strongest Basic)-3.6ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count26ChemAxon
Hydrogen Donor Count17ChemAxon
Polar Surface Area461.43 ŲChemAxon
Rotatable Bond Count48ChemAxon
Refractivity345.28 m³·mol⁻¹ChemAxon
Polarizability152.64 ųChemAxon
Number of Rings4ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash Key
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0gx1-1149041000-4d403300d85c4db33a67View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0a4i-1196028100-2ba755a68c52f9a44b68View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0kv3-2593330000-5797857dd297777bb076View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-001i-0019000000-0b3916c49e89751f7ebaView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0a59-6079012200-4fd8de9bfebd52f8d67eView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0uk9-4091020200-2f2535472e9be48e28bfView in MoNA
Biological Properties
Cellular Locations
  • Cell membrane
  • Endosome
  • Membrane
Biospecimen Locations
  • Brain
  • Neuron
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BrainExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal
  • Not Applicable
 details
NeuronExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal
  • Not Applicable
 details
Abnormal Concentrations
Not Available
HMDB IDHMDB0004937
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB023525
KNApSAcK IDNot Available
Chemspider ID16744923
KEGG Compound IDC04884
BioCyc IDCPD-1100
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN ID7190
PubChem Compound20057333
PDB IDNot Available
ChEBI IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available