Showing metabocard for Ganglioside GD3 (d18:1/26:1(17Z)) (BMDB0004918)

IdentificationTaxonomyPhysical propertiesPathwaysSpectraConcentrationsLinksReferencesXML
Record Information
Version1.0
Creation Date2016-09-30 23:12:53 UTC
Update Date2020-05-11 20:31:55 UTC
BMDB IDBMDB0004918
Secondary Accession Numbers
  • BMDB04918
Metabolite Identification
Common NameGanglioside GD3 (d18:1/26:1(17Z))
DescriptionGanglioside GD3 (d18:1/26:1(17Z)) 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. Ganglioside GD3 (d18:1/26:1(17Z)) is a moderately basic compound (based on its pKa).
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
ValueSource
(2S,4S,5R)-2-{[(1S,2R)-1-[(3R,4S,6S)-6-carboxy-6-{[(2S,3R,4S,5S,6R)-2-{[(2R,3S,4R,5S,6R)-4,5-dihydroxy-6-{[(2S,3R,4E)-3-hydroxy-2-{[(17Z)-1-hydroxyhexacos-17-en-1-ylidene]amino}octadec-4-en-1-yl]oxy}-2-(hydroxymethyl)oxan-3-yl]oxy}-3,5-dihydroxy-6-(hydroxymethyl)oxan-4-yl]oxy}-4-hydroxy-3-[(1-hydroxyethylidene)amino]oxan-2-yl]-1,3-dihydroxypropan-2-yl]oxy}-4-hydroxy-5-[(1-hydroxyethylidene)amino]-6-[(1R,2R)-1,2,3-trihydroxypropyl]oxane-2-carboxylateGenerator
Chemical FormulaC78H139N3O29
Average Molecular Weight1582.962
Monoisotopic Molecular Weight1581.949425468
IUPAC Name(2S,4S,5R)-2-{[(1S,2R)-1-[(3R,4S,6S)-6-carboxy-6-{[(2S,3R,4S,5S,6R)-2-{[(2R,3S,4R,5S,6R)-4,5-dihydroxy-6-{[(2S,3R,4E)-3-hydroxy-2-{[(17Z)-1-hydroxyhexacos-17-en-1-ylidene]amino}octadec-4-en-1-yl]oxy}-2-(hydroxymethyl)oxan-3-yl]oxy}-3,5-dihydroxy-6-(hydroxymethyl)oxan-4-yl]oxy}-4-hydroxy-3-[(1-hydroxyethylidene)amino]oxan-2-yl]-1,3-dihydroxypropan-2-yl]oxy}-4-hydroxy-5-[(1-hydroxyethylidene)amino]-6-[(1R,2R)-1,2,3-trihydroxypropyl]oxane-2-carboxylic acid
Traditional Name(2S,4S,5R)-2-{[(1S,2R)-1-[(3R,4S,6S)-6-carboxy-6-{[(2S,3R,4S,5S,6R)-2-{[(2R,3S,4R,5S,6R)-4,5-dihydroxy-6-{[(2S,3R,4E)-3-hydroxy-2-{[(17Z)-1-hydroxyhexacos-17-en-1-ylidene]amino}octadec-4-en-1-yl]oxy}-2-(hydroxymethyl)oxan-3-yl]oxy}-3,5-dihydroxy-6-(hydroxymethyl)oxan-4-yl]oxy}-4-hydroxy-3-[(1-hydroxyethylidene)amino]oxan-2-yl]-1,3-dihydroxypropan-2-yl]oxy}-4-hydroxy-5-[(1-hydroxyethylidene)amino]-6-[(1R,2R)-1,2,3-trihydroxypropyl]oxane-2-carboxylic acid
CAS Registry NumberNot Available
SMILES
[H]\C(CCCCCCCC)=C(/[H])CCCCCCCCCCCCCCCC(O)=N[C@@]([H])(CO[C@]1([H])O[C@]([H])(CO)[C@@]([H])(O[C@]2([H])O[C@]([H])(CO)[C@]([H])(O)[C@]([H])(O[C@@]3(C[C@]([H])(O)[C@@]([H])(N=C(C)O)C([H])(O3)[C@]([H])(O)[C@@]([H])(CO)O[C@@]3(C[C@]([H])(O)[C@@]([H])(N=C(C)O)C([H])(O3)[C@]([H])(O)[C@]([H])(O)CO)C(O)=O)C(O)=O)[C@@]2([H])O)[C@]([H])(O)[C@]1([H])O)[C@]([H])(O)C(\[H])=C(/[H])CCCCCCCCCCCCC
InChI Identifier
InChI=1S/C78H139N3O29/c1-5-7-9-11-13-15-17-19-20-21-22-23-24-25-26-27-28-30-32-34-36-38-40-42-60(92)81-52(53(88)41-39-37-35-33-31-29-18-16-14-12-10-8-6-2)49-103-73-67(97)66(96)69(59(48-85)105-73)106-74-68(98)72(64(94)57(46-83)104-74)110-78(76(101)102)44-55(90)62(80-51(4)87)71(109-78)65(95)58(47-84)107-77(75(99)100)43-54(89)61(79-50(3)86)70(108-77)63(93)56(91)45-82/h19-20,39,41,52-59,61-74,82-85,88-91,93-98H,5-18,21-38,40,42-49H2,1-4H3,(H,79,86)(H,80,87)(H,81,92)(H,99,100)(H,101,102)/b20-19-,41-39+/t52-,53+,54-,55-,56+,57+,58+,59+,61+,62+,63+,64-,65+,66+,67-,68+,69+,70?,71?,72-,73+,74-,77+,78-/m0/s1
InChI KeyODLSIOMURUFLJN-GAMKTUFHSA-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
  • Dicarboxylic acid or derivatives
  • Fatty amide
  • N-acyl-amine
  • Fatty acyl
  • Oxane
  • Pyran
  • Acetamide
  • Secondary carboxylic acid amide
  • Secondary alcohol
  • Carboxamide group
  • Organoheterocyclic compound
  • Polyol
  • Oxacycle
  • Carboxylic acid derivative
  • Carboxylic acid
  • Acetal
  • Organooxygen compound
  • Organic oxide
  • Alcohol
  • Hydrocarbon derivative
  • Carbonyl group
  • Organic oxygen compound
  • Organic nitrogen compound
  • Primary alcohol
  • Organopnictogen 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
  • Myelin sheath
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP3.95ALOGPS
logP8.21ChemAxon
logS-5ALOGPS
pKa (Strongest Acidic)2.7ChemAxon
pKa (Strongest Basic)2.2ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count32ChemAxon
Hydrogen Donor Count19ChemAxon
Polar Surface Area529.43 ŲChemAxon
Rotatable Bond Count59ChemAxon
Refractivity399.84 m³·mol⁻¹ChemAxon
Polarizability177.63 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, Negativesplash10-03di-1122190010-006529e598081738c796View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0a4r-8259030021-d37e55c27336a6542e86View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0a4i-3559000011-2458fecb7ed8433ac98cView in MoNA
Biological Properties
Cellular Locations
  • Cell membrane
  • Endosome
  • Membrane
  • Myelin sheath
Biospecimen Locations
  • Adrenal Medulla
  • Brain
  • Neuron
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
Adrenal MedullaExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal
  • Not Applicable
 details
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 IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound57511283
PDB IDNot Available
ChEBI IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available