Showing metabocard for Ganglioside GD3 (d18:1/18:1(11Z)) (BMDB0011872)

IdentificationTaxonomyPhysical propertiesPathwaysSpectraConcentrationsLinksReferencesXML
Record Information
Version1.0
Creation Date2016-10-03 18:26:43 UTC
Update Date2020-04-22 15:47:03 UTC
BMDB IDBMDB0011872
Secondary Accession Numbers
  • BMDB11872
Metabolite Identification
Common NameGanglioside GD3 (d18:1/18:1(11Z))
DescriptionGanglioside GD3 (d18:1/18:1(11Z)) 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 (d18:1/18:1(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,4E)-3-hydroxy-2-{[(11Z)-1-hydroxyoctadec-11-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-carboxylateHMDB
Chemical FormulaC70H123N3O29
Average Molecular Weight1470.7283
Monoisotopic Molecular Weight1469.824224989
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]-2-{[(2S,3R,4S,5S,6R)-2-{[(2R,3S,4R,5R,6R)-4,5-dihydroxy-6-{[(2S,3R,4E)-3-hydroxy-2-[(11Z)-octadec-11-enamido]octadec-4-en-1-yl]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,4E)-3-hydroxy-2-[(11Z)-octadec-11-enamido]octadec-4-en-1-yl]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
CCCCCCCCCCCCC\C=C\[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/C70H123N3O29/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/h15,17,31,33,44-51,53-66,74-77,80-83,85-90H,5-14,16,18-30,32,34-41H2,1-4H3,(H,71,78)(H,72,79)(H,73,84)(H,91,92)(H,93,94)/b17-15-,33-31+/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 KeyYTRCMAZBKACTOX-OEZVKBNKSA-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
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP2.17ALOGPS
logP3.05ChemAxon
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 Count51ChemAxon
Refractivity361.46 m³·mol⁻¹ChemAxon
Polarizability161.15 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, Negativesplash10-01c0-5091610000-2a24e68d94366881d864View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-001i-1090200100-3ec0de1cf9cf32a6d7a1View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0l06-9273340531-b9a9e986543ae1c2d48fView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0fft-4411960500-e0637aeeef333d899d18View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-074j-0130530900-8a2385581485310c3bc7View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0006-1923340200-34a3932e35138beb88e0View in MoNA
Biological Properties
Cellular Locations
  • Cell membrane
  • Endosome
  • Membrane
Biospecimen LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
HMDB IDHMDB0011872
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB028541
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound53481148
PDB IDNot Available
ChEBI IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available