Showing metabocard for Ganglioside GD1b (d18:1/16:0) (BMDB0011824)

IdentificationTaxonomyPhysical propertiesPathwaysSpectraConcentrationsLinksReferencesXML
Record Information
Version1.0
Creation Date2016-10-03 18:25:34 UTC
Update Date2020-04-22 15:46:45 UTC
BMDB IDBMDB0011824
Secondary Accession Numbers
  • BMDB11824
Metabolite Identification
Common NameGanglioside GD1b (d18:1/16:0)
DescriptionGanglioside GD1b (d18:1/16:0) 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 GD1b (d18:1/16:0) 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,4R,5S,6R)-2-{[(2R,3S,4R,5R,6R)-4,5-dihydroxy-6-{[(2S,3R)-3-hydroxy-2-[(1-hydroxyhexadecylidene)amino]octadec-4-en-1-yl]oxy}-2-(hydroxymethyl)oxan-3-yl]oxy}-3-hydroxy-5-{[(2S,3R,4R,5R,6R)-5-hydroxy-6-(hydroxymethyl)-3-(2-oxopropyl)-4-{[(2R,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxan-2-yl]oxy}-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-carboxylateGenerator
Chemical FormulaC83H145N3O39
Average Molecular Weight1809.0361
Monoisotopic Molecular Weight1807.945521913
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,4R,5S,6R)-2-{[(2R,3S,4R,5R,6R)-6-{[(2S,3R,4E)-2-hexadecanamido-3-hydroxyoctadec-4-en-1-yl]oxy}-4,5-dihydroxy-2-(hydroxymethyl)oxan-3-yl]oxy}-3-hydroxy-5-{[(2S,3R,4R,5R,6R)-5-hydroxy-6-(hydroxymethyl)-3-(2-oxopropyl)-4-{[(2R,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxan-2-yl]oxy}-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,4R,5S,6R)-2-{[(2R,3S,4R,5R,6R)-6-{[(2S,3R,4E)-2-hexadecanamido-3-hydroxyoctadec-4-en-1-yl]oxy}-4,5-dihydroxy-2-(hydroxymethyl)oxan-3-yl]oxy}-3-hydroxy-5-{[(2S,3R,4R,5R,6R)-5-hydroxy-6-(hydroxymethyl)-3-(2-oxopropyl)-4-{[(2R,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxan-2-yl]oxy}-6-(hydroxymethyl)oxan-4-yl]oxy}-4-hydroxyoxane-2-carboxylic acid
CAS Registry NumberNot Available
SMILES
CCCCCCCCCCCCCCCC(=O)N[C@@H](CO[C@@H]1O[C@H](CO)[C@@H](O[C@@H]2O[C@H](CO)[C@H](O[C@@H]3O[C@H](CO)[C@H](O)[C@H](O[C@@H]4O[C@H](CO)[C@H](O)[C@H](O)[C@H]4O)[C@H]3CC(C)=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)[C@H](O)\C=C\CCCCCCCCCCCCC
InChI Identifier
InChI=1S/C83H145N3O39/c1-6-8-10-12-14-16-18-20-22-24-26-28-30-32-49(96)48(86-58(100)33-31-29-27-25-23-21-19-17-15-13-11-9-7-2)43-114-77-68(108)66(106)71(56(41-91)117-77)120-79-69(109)75(72(57(42-92)118-79)121-76-47(34-44(3)93)70(63(103)54(39-89)115-76)119-78-67(107)65(105)62(102)53(38-88)116-78)125-83(81(112)113)36-51(98)60(85-46(5)95)74(124-83)64(104)55(40-90)122-82(80(110)111)35-50(97)59(84-45(4)94)73(123-82)61(101)52(99)37-87/h30,32,47-57,59-79,87-92,96-99,101-109H,6-29,31,33-43H2,1-5H3,(H,84,94)(H,85,95)(H,86,100)(H,110,111)(H,112,113)/b32-30+/t47-,48+,49-,50+,51+,52-,53-,54-,55-,56-,57-,59-,60-,61-,62+,63+,64-,65+,66-,67-,68-,69-,70-,71-,72+,73?,74?,75-,76+,77-,78+,79+,82-,83+/m1/s1
InChI KeyGRGARPRHAYNQDP-HPUFLENBSA-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
  • 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
  • Fatty acyl
  • Fatty amide
  • Pyran
  • Oxane
  • N-acyl-amine
  • Acetamide
  • Ketone
  • Secondary alcohol
  • Carboxamide group
  • Secondary carboxylic acid amide
  • 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
logP1.04ALOGPS
logP-0.29ChemAxon
logS-3.4ALOGPS
pKa (Strongest Acidic)2.46ChemAxon
pKa (Strongest Basic)-3.7ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count39ChemAxon
Hydrogen Donor Count24ChemAxon
Polar Surface Area674.1 ŲChemAxon
Rotatable Bond Count58ChemAxon
Refractivity428.9 m³·mol⁻¹ChemAxon
Polarizability192.96 ųChemAxon
Number of Rings6ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
SpectraNot Available
Biological Properties
Cellular Locations
  • Cell membrane
  • Endosome
  • Membrane
Biospecimen LocationsNot Available
Pathways
Normal Concentrations
Not Available
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 Compound53481100
PDB IDNot Available
ChEBI IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available