Showing metabocard for Ganglioside GM3 (d18:1/12:0) (BMDB0004842)

IdentificationTaxonomyPhysical propertiesPathwaysSpectraConcentrationsLinksReferencesXML
Record Information
Version1.0
Creation Date2016-09-30 23:11:04 UTC
Update Date2020-05-11 20:56:24 UTC
BMDB IDBMDB0004842
Secondary Accession Numbers
  • BMDB04842
Metabolite Identification
Common NameGanglioside GM3 (d18:1/12:0)
DescriptionGanglioside GM3 (d18:1/12:0) is a moderately basic compound (based on its pKa).
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
ValueSource
(2S,4S,5R)-2-{[(2S,3R,4S,5S,6R)-2-{[(2R,3S,4R,5S,6R)-4,5-dihydroxy-6-{[(2S,3R)-3-hydroxy-2-[(1-hydroxydodecylidene)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-carboxylateGenerator
Chemical FormulaC53H96N2O21
Average Molecular Weight1097.344
Monoisotopic Molecular Weight1096.650558119
IUPAC Name(2S,4S,5R)-2-{[(2S,3R,4S,5S,6R)-2-{[(2R,3S,4R,5S,6R)-4,5-dihydroxy-6-{[(2S,3R,4E)-3-hydroxy-2-[(1-hydroxydodecylidene)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-carboxylic acid
Traditional Name(2S,4S,5R)-2-{[(2S,3R,4S,5S,6R)-2-{[(2R,3S,4R,5S,6R)-4,5-dihydroxy-6-{[(2S,3R,4E)-3-hydroxy-2-[(1-hydroxydodecylidene)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-carboxylic acid
CAS Registry NumberNot Available
SMILES
[H]C(CCCCCCCCCCCCC)=C([H])[C@@]([H])(O)[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])(O)CO)C(O)=O)[C@@]2([H])O)[C@]([H])(O)[C@]1([H])O)N=C(O)CCCCCCCCCCC
InChI Identifier
InChI=1S/C53H96N2O21/c1-4-6-8-10-12-14-15-16-17-19-20-22-24-26-35(60)34(55-40(63)27-25-23-21-18-13-11-9-7-5-2)32-71-50-45(67)44(66)47(39(31-58)73-50)74-51-46(68)49(43(65)38(30-57)72-51)76-53(52(69)70)28-36(61)41(54-33(3)59)48(75-53)42(64)37(62)29-56/h24,26,34-39,41-51,56-58,60-62,64-68H,4-23,25,27-32H2,1-3H3,(H,54,59)(H,55,63)(H,69,70)/b26-24+/t34-,35+,36-,37+,38+,39+,41+,42+,43-,44+,45-,46+,47+,48?,49-,50+,51-,53-/m0/s1
InChI KeyWWDJRYLWFWMNJE-XDBBIGAJSA-N
Chemical Taxonomy
ClassificationNot classified
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
logP2.91ALOGPS
logP4.19ChemAxon
logS-4.4ALOGPS
pKa (Strongest Acidic)3.06ChemAxon
pKa (Strongest Basic)2.51ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count23ChemAxon
Hydrogen Donor Count14ChemAxon
Polar Surface Area380.39 ŲChemAxon
Rotatable Bond Count39ChemAxon
Refractivity273.51 m³·mol⁻¹ChemAxon
Polarizability122.18 ųChemAxon
Number of Rings3ChemAxon
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, Positivesplash10-01t9-9000205120-80a2255a3654c4e1abe9View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-000i-2100407930-1288e967b227e23730d4View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-08fu-4421409120-c7018a7922186e534935View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-00ou-9110001010-b7ec15380929cfffe26bView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-052o-9343104020-b6c35a29a70654f182f4View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0a4l-9844024000-53e467cffcdd16b7b2e7View in MoNA
Biological Properties
Cellular Locations
  • Cell membrane
  • Endosome
  • Membrane
  • Myelin sheath
Biospecimen Locations
  • Adrenal Gland
  • Brain
  • Epidermis
  • Fibroblasts
  • Neuron
  • Testis
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
Adrenal GlandExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal
  • Not Applicable
 details
BrainExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal
  • Not Applicable
 details
EpidermisExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal
  • Not Applicable
 details
FibroblastsExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal
  • Not Applicable
 details
NeuronExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal
  • Not Applicable
 details
TestisExpected 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 CompoundNot Available
PDB IDNot Available
ChEBI IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available