Showing metabocard for Ganglioside GD3 (d18:0/18:1(11Z)) (BMDB0011860)

IdentificationTaxonomyPhysical propertiesPathwaysSpectraConcentrationsLinksReferencesXML
Record Information
Version1.0
Creation Date2016-10-03 18:26:26 UTC
Update Date2020-04-22 15:46:58 UTC
BMDB IDBMDB0011860
Secondary Accession Numbers
  • BMDB11860
Metabolite Identification
Common NameGanglioside GD3 (d18:0/18:1(11Z))
DescriptionGanglioside GD3 (d18:0/18:1(11Z)) belongs to the class of organic compounds known as glycosphingolipids. These are sphingolipids containing a saccharide moiety glycosidically attached to the sphingoid base. Although saccharide moieties are mostly O-glycosidically linked to the ceramide moiety, other sphingolipids with glycosidic bonds of other types (e.g. S-,C-, or N-type) has been reported. Ganglioside GD3 (d18:0/18:1(11Z)) is an extremely weak basic (essentially neutral) 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,5R,6R)-4,5-dihydroxy-6-{[(2S,3R)-3-hydroxy-2-{[(11Z)-1-hydroxyoctadec-11-en-1-ylidene]amino}octadecyl]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-carboxylateHMDB
Chemical FormulaC70H125N3O29
Average Molecular Weight1472.7442
Monoisotopic Molecular Weight1471.839875053
IUPAC Name(2S,4S,5R)-6-[(1S,2R)-2-{[(2S,4S,5R)-2-carboxy-5-acetamido-4-hydroxy-6-[(1R,2R)-1,2,3-trihydroxypropyl]oxan-2-yl]oxy}-1,3-dihydroxypropyl]-2-{[(2S,3R,4S,5S,6R)-2-{[(2R,3S,4R,5R,6R)-4,5-dihydroxy-6-{[(2S,3R)-3-hydroxy-2-[(11Z)-octadec-11-enamido]octadecyl]oxy}-2-(hydroxymethyl)oxan-3-yl]oxy}-3,5-dihydroxy-6-(hydroxymethyl)oxan-4-yl]oxy}-5-acetamido-4-hydroxyoxane-2-carboxylic acid
Traditional Name(2S,4S,5R)-6-[(1S,2R)-2-{[(2S,4S,5R)-2-carboxy-5-acetamido-4-hydroxy-6-[(1R,2R)-1,2,3-trihydroxypropyl]oxan-2-yl]oxy}-1,3-dihydroxypropyl]-2-{[(2S,3R,4S,5S,6R)-2-{[(2R,3S,4R,5R,6R)-4,5-dihydroxy-6-{[(2S,3R)-3-hydroxy-2-[(11Z)-octadec-11-enamido]octadecyl]oxy}-2-(hydroxymethyl)oxan-3-yl]oxy}-3,5-dihydroxy-6-(hydroxymethyl)oxan-4-yl]oxy}-5-acetamido-4-hydroxyoxane-2-carboxylic acid
CAS Registry NumberNot Available
SMILES
CCCCCCCCCCCCCCC[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](O[C@@]3(C[C@H](O)[C@@H](NC(C)=O)C(O3)[C@H](O)[C@@H](CO)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(O)=O)[C@H]2O)[C@H](O)[C@H]1O)NC(=O)CCCCCCCCC\C=C/CCCCCC
InChI Identifier
InChI=1S/C70H125N3O29/c1-5-7-9-11-13-15-17-19-20-22-24-26-28-30-32-34-52(84)73-44(45(80)33-31-29-27-25-23-21-18-16-14-12-10-8-6-2)41-95-65-59(89)58(88)61(51(40-77)97-65)98-66-60(90)64(56(86)49(38-75)96-66)102-70(68(93)94)36-47(82)54(72-43(4)79)63(101-70)57(87)50(39-76)99-69(67(91)92)35-46(81)53(71-42(3)78)62(100-69)55(85)48(83)37-74/h15,17,44-51,53-66,74-77,80-83,85-90H,5-14,16,18-41H2,1-4H3,(H,71,78)(H,72,79)(H,73,84)(H,91,92)(H,93,94)/b17-15-/t44-,45+,46-,47-,48+,49+,50+,51+,53+,54+,55+,56-,57+,58+,59+,60+,61+,62?,63?,64-,65+,66-,69+,70-/m0/s1
InChI KeyONIRRRFTPWTIDH-TUWAOKQNSA-N
Chemical Taxonomy
Description belongs to the class of organic compounds known as glycosphingolipids. These are sphingolipids containing a saccharide moiety glycosidically attached to the sphingoid base. Although saccharide moieties are mostly O-glycosidically linked to the ceramide moiety, other sphingolipids with glycosidic bonds of other types (e.g. S-,C-, or N-type) has been reported.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassSphingolipids
Sub ClassGlycosphingolipids
Direct ParentGlycosphingolipids
Alternative Parents
Substituents
  • Glycosphingolipid
  • Oligosaccharide
  • N-acylneuraminic acid
  • N-acylneuraminic acid or derivatives
  • Neuraminic acid
  • Fatty acyl glycoside
  • C-glucuronide
  • Alkyl glycoside
  • C-glycosyl compound
  • O-glycosyl compound
  • Glycosyl compound
  • Ketal
  • Dicarboxylic acid or derivatives
  • Pyran
  • N-acyl-amine
  • Oxane
  • Fatty amide
  • Fatty acyl
  • Acetamide
  • Carboxamide group
  • Secondary carboxylic acid amide
  • Secondary alcohol
  • Acetal
  • Carboxylic acid derivative
  • Carboxylic acid
  • Oxacycle
  • Organoheterocyclic compound
  • Polyol
  • Hydrocarbon derivative
  • Alcohol
  • Organic oxide
  • Carbonyl group
  • Organic nitrogen compound
  • Organic oxygen compound
  • Primary alcohol
  • Organopnictogen compound
  • Organooxygen 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 SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP2.09ALOGPS
logP3.25ChemAxon
logS-4.2ALOGPS
pKa (Strongest Acidic)2.45ChemAxon
pKa (Strongest Basic)-3.7ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count29ChemAxon
Hydrogen Donor Count19ChemAxon
Polar Surface Area518.96 ŲChemAxon
Rotatable Bond Count52ChemAxon
Refractivity360.5 m³·mol⁻¹ChemAxon
Polarizability162.79 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, Positivesplash10-0fdk-2511960500-cd5ea86d66c5b8750d8fView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03ka-0230530900-b58a66cee3b7f39ae945View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-008c-4935550300-dbcddf391a1e87ab1fd8View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-00di-5091710000-2457cef4956e3a8bd6f4View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-001i-1090200100-5b04f327c0725f01709bView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-054o-9274350330-41cf08e9b7c409c693f5View in MoNA
Biological Properties
Cellular Locations
  • Cell membrane
  • Endosome
  • Membrane
Biospecimen LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
HMDB IDHMDB0011860
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB028529
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound53481136
PDB IDNot Available
ChEBI IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available