Showing metabocard for Cer(d18:0/20:1(11Z)) (BMDB0063622)

IdentificationTaxonomyPhysical propertiesSpectraConcentrationsLinksReferencesXML
Record Information
Version1.0
Creation Date2018-10-10 21:42:31 UTC
Update Date2020-06-04 19:22:32 UTC
MCDB ID BMDB0063622
Secondary Accession Numbers
  • BMDB63622
Metabolite Identification
Common NameCer(d18:0/20:1(11Z))
DescriptionCer(d18:0/20:1(11Z)), also known as N-11Z-eicosenoyl-sphinganine, is a ceramide (Cer). Ceramides are members of the class of compounds known as sphingolipids (SPs), or glycosylceramides. SPs are lipids containing a backbone of sphingoid bases (e.g. sphingosine or sphinganine) that are often covalently bound to a fatty acid derivative through N-acylation. SPs are found in cell membranes, particularly in peripheral nerve cells and the cells found in the central nervous system (including the brain and spinal cord). Sphingolipids are extremely versatile molecules that have functions controlling fundamental cellular processes such as cell division, differentiation, and cell death. Impairments associated with sphingolipid metabolism are associated with many common human diseases such as diabetes, various cancers, microbial infections, diseases of the cardiovascular and respiratory systems, Alzheimer’s disease and other neurological syndromes. The biosynthesis and catabolism of sphingolipids involves a large number of intermediate metabolites where many different enzymes are involved. Simple sphingolipids, which include the sphingoid bases and ceramides, make up the early products of the sphingolipid synthetic pathways, while complex sphingolipids may be formed by the addition of head groups to the ceramide template (Wikipedia). In humans, ceramides are phosphorylated to ceramide phosphates (CerPs) through the action of a specific ceramide kinase (CerK). Ceramide phosphates are important metabolites of ceramides as they act as a mediators of the inflammatory response. Ceramides are also one of the hydrolysis byproducts of sphingomyelins (SMs) through the action of the enzyme sphingomyelin phosphodiesterase, which has been identified in the subcellular fractions of human epidermis (PMID: 25935 ) and many other tissues. Ceramides can also be synthesized from serine and palmitate in a de novo pathway and are regarded as important cellular signals for inducing apoptosis (PMID: 14998372 ). Ceramides are key in the biosynthesis of glycosphingolipids and gangliosides. In terms of its appearance and structure, Cer(d18:0/20:1(11Z)) is a colorless solid that consists of a saturated 18-carbon sphingoid base with an attached unsaturated 11Z-eicosenoyl fatty acid side chain. In most mammalian SPs, the 18-carbon sphingoid bases are predominant (PMID: 9759481 ).
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
ValueSource
CeramideMetBuilder
N-(11Z-Eicosenoyl)-sphinganineMetBuilder
Ceramide(D18:0/20:1(11Z))MetBuilder
N-(11Z-Eicosenoyl)-dihydrosphingosineMetBuilder
N-(11Z-Eicosenoyl)-D-erythro-sphinganineMetBuilder
Chemical FormulaC38H75NO3
Average Molecular Weight594.022
Monoisotopic Molecular Weight593.574695279
IUPAC Name(11Z)-N-[(2S)-1,3-dihydroxyoctadecan-2-yl]icos-11-enamide
Traditional Name(11Z)-N-[(2S)-1,3-dihydroxyoctadecan-2-yl]icos-11-enamide
CAS Registry NumberNot Available
SMILES
CCCCCCCCCCCCCCCC(O)[C@H](CO)NC(=O)CCCCCCCCC\C=C/CCCCCCCC
InChI Identifier
InChI=1S/C38H75NO3/c1-3-5-7-9-11-13-15-17-18-19-20-22-24-26-28-30-32-34-38(42)39-36(35-40)37(41)33-31-29-27-25-23-21-16-14-12-10-8-6-4-2/h17-18,36-37,40-41H,3-16,19-35H2,1-2H3,(H,39,42)/b18-17-/t36-,37?/m0/s1
InChI KeyPULBITQLTXYVQX-VQNGLQQLSA-N
Chemical Taxonomy
Description belongs to the class of organic compounds known as long-chain ceramides. These are ceramides bearing a long chain fatty acid.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassSphingolipids
Sub ClassCeramides
Direct ParentLong-chain ceramides
Alternative Parents
Substituents
  • Long-chain ceramide
  • Fatty amide
  • N-acyl-amine
  • Fatty acyl
  • Carboxamide group
  • Secondary carboxylic acid amide
  • Secondary alcohol
  • Carboxylic acid derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Hydrocarbon derivative
  • Organic oxide
  • Organic oxygen compound
  • Alcohol
  • Organic nitrogen compound
  • Carbonyl group
  • Primary alcohol
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP10.04ALOGPS
logP12.49ChemAxon
logS-7.4ALOGPS
pKa (Strongest Acidic)13.83ChemAxon
pKa (Strongest Basic)-1ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area69.56 ŲChemAxon
Rotatable Bond Count34ChemAxon
Refractivity184.33 m³·mol⁻¹ChemAxon
Polarizability80.49 ųChemAxon
Number of Rings0ChemAxon
Bioavailability0ChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Spectra
Not Available
Concentrations
StatusValueReferenceDetails
Detected and Quantified0.07 +/- 0.01 uM details
Detected and Quantified0.12 +/- 0.01 uM details
Detected and Quantified0.144 +/- 0.002 uM details
Detected and Quantified0.22 +/- 0.01 uM details
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB 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 Compound89054488
PDB IDNot Available
ChEBI IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Dickson RC: Sphingolipid functions in Saccharomyces cerevisiae: comparison to mammals. Annu Rev Biochem. 1998;67:27-48. doi: 10.1146/annurev.biochem.67.1.27. [PubMed:9759481 ]
  2. Bowser PA, Gray GM: Sphingomyelinase in pig and human epidermis. J Invest Dermatol. 1978 Jun;70(6):331-5. [PubMed:25935 ]
  3. Tserng KY, Griffin RL: Ceramide metabolite, not intact ceramide molecule, may be responsible for cellular toxicity. Biochem J. 2004 Jun 15;380(Pt 3):715-22. doi: 10.1042/BJ20031733. [PubMed:14998372 ]