Showing metabocard for Cer(d20:0/22:2(6Z,13Z)) (BMDB0063624)

IdentificationTaxonomyPhysical propertiesSpectraConcentrationsLinksReferencesXML
Record Information
Version1.0
Creation Date2018-10-10 21:42:42 UTC
Update Date2020-06-04 19:28:58 UTC
MCDB ID BMDB0063624
Secondary Accession Numbers
  • BMDB63624
Metabolite Identification
Common NameCer(d20:0/22:2(6Z,13Z))
DescriptionCer(d20:0/22:2(6Z,13Z)), also known as N-6Z,13Z-docosadienoyl-eicosasphinganine, 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(d20:0/22:2(6Z,13Z)) is a colorless solid that consists of a saturated 20-carbon sphingoid base with an attached unsaturated 6Z,13Z-docosadienoyl fatty acid side chain. In most mammalian SPs, the 18-carbon sphingoid bases are predominant (PMID: 9759481 ).
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
ValueSource
(6Z,13Z)-N-[(2S)-1,3-Dihydroxyicosan-2-yl]docosa-6,13-dienimidateGenerator
Chemical FormulaC42H81NO3
Average Molecular Weight648.114
Monoisotopic Molecular Weight647.621645472
IUPAC Name(6Z,13Z)-N-[(2S)-1,3-dihydroxyicosan-2-yl]docosa-6,13-dienamide
Traditional Name(6Z,13Z)-N-[(2S)-1,3-dihydroxyicosan-2-yl]docosa-6,13-dienamide
CAS Registry NumberNot Available
SMILES
CCCCCCCCCCCCCCCCCC(O)[C@H](CO)NC(=O)CCCC\C=C/CCCCC\C=C/CCCCCCCC
InChI Identifier
InChI=1S/C42H81NO3/c1-3-5-7-9-11-13-15-17-19-20-21-22-24-26-28-30-32-34-36-38-42(46)43-40(39-44)41(45)37-35-33-31-29-27-25-23-18-16-14-12-10-8-6-4-2/h17,19,28,30,40-41,44-45H,3-16,18,20-27,29,31-39H2,1-2H3,(H,43,46)/b19-17-,30-28-/t40-,41?/m0/s1
InChI KeyABZIJOKCYYZWFJ-QWKKJKGWSA-N
Chemical Taxonomy
Description belongs to the class of organic compounds known as secondary alcohols. Secondary alcohols are compounds containing a secondary alcohol functional group, with the general structure HOC(R)(R') (R,R'=alkyl, aryl).
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassAlcohols and polyols
Direct ParentSecondary alcohols
Alternative Parents
Substituents
  • Secondary alcohol
  • Organic 1,3-dipolar compound
  • Propargyl-type 1,3-dipolar organic compound
  • Carboximidic acid derivative
  • Carboximidic acid
  • Organic nitrogen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Primary alcohol
  • Organonitrogen compound
  • 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
logP10.44ALOGPS
logP13.9ChemAxon
logS-7.6ALOGPS
pKa (Strongest Acidic)13.81ChemAxon
pKa (Strongest Basic)-1ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area69.56 ŲChemAxon
Rotatable Bond Count37ChemAxon
Refractivity203.85 m³·mol⁻¹ChemAxon
Polarizability87.43 ųChemAxon
Number of Rings0ChemAxon
Bioavailability0ChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Spectra
Spectrum TypeDescriptionSplash KeyDeposition DateView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-01q9-0004009000-4c37b6df9cb14c0fa7992019-02-22View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-1039015000-cd3d61d2dcd75590d9842019-02-22View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-01ox-2293330000-4d6f0086e433e594f7fd2019-02-22View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0002-0001009000-6ae65b5b927d4f3b37df2019-02-23View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-02bb-0019026000-ab313fed3de9314882b12019-02-23View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-06ry-7159000000-72dec8e5b6ba93a0cc812019-02-23View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0002-0000009000-8034b399a95d3586d3662021-10-21View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0005-0050009000-785eab6ea462de30030e2021-10-21View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-01po-0085009000-70f522c4571402e3936a2021-10-21View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0udi-0000009000-31264534e837f791da652021-10-21View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0udi-0000009000-31264534e837f791da652021-10-21View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-000i-0000009000-68b46d0682c146d495b72021-10-21View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0002-0000009000-99b30254d9b8ff6d778b2021-10-21View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0002-0001009000-31f0b96ad1bbd84d55ee2021-10-21View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-03dj-0004009000-c588fe94b61a2e0870782021-10-21View Spectrum
Concentrations
StatusValueReferenceDetails
Detected and Quantified0.052 +/- 0.002 uM details
Detected and Quantified0.262 +/- 0.004 uM details
Detected and Quantified0.357 +/- 0.002 uM details
Detected and Quantified0.47 +/- 0.01 uM details
HMDB IDHMDB0304644
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 CompoundNot Available
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 ]