Showing metabocard for Ganglioside GD3 (d18:0/16:0) (BMDB0011858)

IdentificationTaxonomyPhysical propertiesPathwaysSpectraConcentrationsLinksReferencesXML
Record Information
Version1.0
Creation Date2016-10-03 18:26:24 UTC
Update Date2020-04-22 15:46:57 UTC
BMDB IDBMDB0011858
Secondary Accession Numbers
  • BMDB11858
Metabolite Identification
Common NameGanglioside GD3 (d18:0/16:0)
DescriptionGanglioside GD3 (d18:0/16:0) 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 (d18:0/16:0) 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-[(1-hydroxyhexadecylidene)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 FormulaC68H123N3O29
Average Molecular Weight1446.7069
Monoisotopic Molecular Weight1445.824224989
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]-5-acetamido-2-{[(2S,3R,4S,5S,6R)-2-{[(2R,3S,4R,5R,6R)-6-{[(2S,3R)-2-hexadecanamido-3-hydroxyoctadecyl]oxy}-4,5-dihydroxy-2-(hydroxymethyl)oxan-3-yl]oxy}-3,5-dihydroxy-6-(hydroxymethyl)oxan-4-yl]oxy}-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]-5-acetamido-2-{[(2S,3R,4S,5S,6R)-2-{[(2R,3S,4R,5R,6R)-6-{[(2S,3R)-2-hexadecanamido-3-hydroxyoctadecyl]oxy}-4,5-dihydroxy-2-(hydroxymethyl)oxan-3-yl]oxy}-3,5-dihydroxy-6-(hydroxymethyl)oxan-4-yl]oxy}-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)CCCCCCCCCCCCCCC
InChI Identifier
InChI=1S/C68H123N3O29/c1-5-7-9-11-13-15-17-19-21-23-25-27-29-31-43(78)42(71-50(82)32-30-28-26-24-22-20-18-16-14-12-10-8-6-2)39-93-63-57(87)56(86)59(49(38-75)95-63)96-64-58(88)62(54(84)47(36-73)94-64)100-68(66(91)92)34-45(80)52(70-41(4)77)61(99-68)55(85)48(37-74)97-67(65(89)90)33-44(79)51(69-40(3)76)60(98-67)53(83)46(81)35-72/h42-49,51-64,72-75,78-81,83-88H,5-39H2,1-4H3,(H,69,76)(H,70,77)(H,71,82)(H,89,90)(H,91,92)/t42-,43+,44-,45-,46+,47+,48+,49+,51+,52+,53+,54-,55+,56+,57+,58+,59+,60?,61?,62-,63+,64-,67+,68-/m0/s1
InChI KeyNCVFCBJVZVKMER-NMYWPWINSA-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
logP1.71ALOGPS
logP2.73ChemAxon
logS-4.1ALOGPS
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 Count51ChemAxon
Refractivity350.18 m³·mol⁻¹ChemAxon
Polarizability160.25 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, Negativesplash10-0006-6091710100-263a1280a559e882d624View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-001i-2091101000-abc5574e2a9fb9b952baView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0pbc-9283250330-36c70fbaa524eccf37ceView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-002b-3121950400-1fc8dd487691efb1133dView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0231-1350945800-7d0bae685d174b80e951View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0a4m-9786620300-fff5dd76f76f48aac902View in MoNA
Biological Properties
Cellular Locations
  • Cell membrane
  • Endosome
  • Membrane
Biospecimen LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
HMDB IDHMDB0011858
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB028527
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound53481134
PDB IDNot Available
ChEBI IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available