Showing metabocard for Ganglioside GM3 (d18:1/25:0) (BMDB0004852)

IdentificationTaxonomyPhysical propertiesPathwaysSpectraConcentrationsLinksReferencesXML
Record Information
Version1.0
Creation Date2016-09-30 23:11:20 UTC
Update Date2020-05-11 20:56:33 UTC
BMDB IDBMDB0004852
Secondary Accession Numbers
  • BMDB04852
Metabolite Identification
Common NameGanglioside GM3 (d18:1/25:0)
DescriptionGanglioside GM3 (d18:1/25:0) 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,4E)-3-hydroxy-2-[(1-hydroxypentacosylidene)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 FormulaC66H122N2O21
Average Molecular Weight1279.695
Monoisotopic Molecular Weight1278.854008956
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-hydroxypentacosylidene)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-hydroxypentacosylidene)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)CCCCCCCCCCCCCCCCCCCCCCCC
InChI Identifier
InChI=1S/C66H122N2O21/c1-4-6-8-10-12-14-16-18-19-20-21-22-23-24-25-26-28-30-32-34-36-38-40-53(76)68-47(48(73)39-37-35-33-31-29-27-17-15-13-11-9-7-5-2)45-84-63-58(80)57(79)60(52(44-71)86-63)87-64-59(81)62(56(78)51(43-70)85-64)89-66(65(82)83)41-49(74)54(67-46(3)72)61(88-66)55(77)50(75)42-69/h37,39,47-52,54-64,69-71,73-75,77-81H,4-36,38,40-45H2,1-3H3,(H,67,72)(H,68,76)(H,82,83)/b39-37+/t47-,48+,49-,50+,51+,52+,54+,55+,56-,57+,58-,59+,60+,61?,62-,63+,64-,66-/m0/s1
InChI KeyASEFIJLVWPPUEV-HDONEROMSA-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
logP5.48ALOGPS
logP9.97ChemAxon
logS-4.9ALOGPS
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 Count52ChemAxon
Refractivity333.33 m³·mol⁻¹ChemAxon
Polarizability150.19 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, Positivesplash10-08i3-0090001053-d36101d9fe7c36b1a1ebView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-00di-1010004049-b09fccdaab150a2e9f80View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-08i9-3235104093-c000b2ba5207ca9ad746View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0a4m-3391001010-b36f9911ee29385f5aacView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0a4r-9473000042-1976f936a61db465ad61View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0ab9-9745000240-c89d02a0addd44a61390View 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