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Record Information
Version4.0
StatusDetected and Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2019-12-04 21:49:27 UTC
HMDB IDHMDB0000950
Secondary Accession Numbers
  • HMDB0011776
  • HMDB00950
  • HMDB11776
Metabolite Identification
Common NameCer(d18:1/23:0)
DescriptionCer(d18:1/23:0), also known as N-tricosanoyl-sphing-4-enine, 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(d18:1/23:0) is a colorless solid that consists of an unsaturated 18-carbon sphingoid base with an attached saturated tricosanoyl fatty acid side chain. In most mammalian SPs, the 18-carbon sphingoid bases are predominant (PMID: 9759481 ).
Structure
Data?1575496167
Synonyms
ValueSource
N-(Tricosanoyl)-sphing-4-enineChEBI
N-[(1S,2R,3E)-2-Hydroxy-1-(hydroxymethyl)-3-heptadecen-1-yl]-tricosanamideHMDB
N-[(1S,2R,3E)-2-Hydroxy-1-(hydroxymethyl)-3-heptadecenyl]-tricosanamideHMDB
[R-[R*,s*-(e)]]-N-[2-hydroxy-1-(hydroxymethyl)-3-heptadecenyl]-tricosanamideHMDB
CeramideHMDB
Ceramide(D18:1/23:0)HMDB
N-(Tricosanoyl)-sphingosineHMDB
N-(Tricosanoyl)-D-erythro-sphingosineHMDB
N-(Tricosanoyl)-4-sphingenineHMDB
N-(Tricosanoyl)-D-sphingosineHMDB
N-(Tricosanoyl)-sphingenineHMDB
N-(Tricosanoyl)-erythro-4-sphingenineHMDB
C23-CeramideHMDB
Cer(d18:1/23:0)HMDB
Ceramide (d18:1,C23:0)HMDB
Chemical FormulaC41H81NO3
Average Molecular Weight636.0867
Monoisotopic Molecular Weight635.621645463
IUPAC NameN-[(2S,3R,4E)-1,3-dihydroxyoctadec-4-en-2-yl]tricosanamide
Traditional NameN-[(2S,3R,4E)-1,3-dihydroxyoctadec-4-en-2-yl]tricosanamide
CAS Registry Number67605-84-9
SMILES
CCCCCCCCCCCCCCCCCCCCCCC(=O)N[C@@H](CO)[C@H](O)\C=C\CCCCCCCCCCCCC
InChI Identifier
InChI=1S/C41H81NO3/c1-3-5-7-9-11-13-15-17-18-19-20-21-22-23-25-27-29-31-33-35-37-41(45)42-39(38-43)40(44)36-34-32-30-28-26-24-16-14-12-10-8-6-4-2/h34,36,39-40,43-44H,3-33,35,37-38H2,1-2H3,(H,42,45)/b36-34+/t39-,40+/m0/s1
InChI KeyNAJHAHQNQCNWOP-PUYNVXOJSA-N
Chemical Taxonomy
Description belongs to the class of organic compounds known as ceramides. These are lipid molecules containing a sphingosine in which the amine group is linked to a fatty acid.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassSphingolipids
Sub ClassCeramides
Direct ParentCeramides
Alternative Parents
Substituents
  • Ceramide
  • Fatty amide
  • N-acyl-amine
  • Fatty acyl
  • Carboxamide group
  • Secondary alcohol
  • Secondary carboxylic acid amide
  • Carboxylic acid derivative
  • Primary alcohol
  • Organooxygen compound
  • Organonitrogen compound
  • Organic oxide
  • Organopnictogen compound
  • Organic oxygen compound
  • Alcohol
  • Organic nitrogen compound
  • Carbonyl group
  • Hydrocarbon derivative
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effect

Health effect:

Organoleptic effect:

Disposition

Route of exposure:

Source:

Biological location:

Process

Naturally occurring process:

Role

Industrial application:

Biological role:

Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility2.4e-05 g/LALOGPS
logP10.29ALOGPS
logP13.98ChemAxon
logS-7.4ALOGPS
pKa (Strongest Acidic)13.62ChemAxon
pKa (Strongest Basic)0.02ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area69.56 ŲChemAxon
Rotatable Bond Count37ChemAxon
Refractivity197.98 m³·mol⁻¹ChemAxon
Polarizability87.82 ųChemAxon
Number of Rings0ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-000i-0000009000-d3e8008e7ba10d1c9431JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-01p9-0050009000-3766eaf41ece7db39bd6JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03yi-0090005000-316946107e778fc6c5c6JSpectraViewer
Biological Properties
Cellular Locations
  • Extracellular
  • Membrane
Biospecimen Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified0.281 +/- 0.033 uMAdult (>18 years old)BothNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB022334
KNApSAcK IDNot Available
Chemspider ID24765757
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN ID5896
PubChem Compound52931115
PDB IDNot Available
ChEBI ID84372
Food Biomarker OntologyNot Available
VMH IDNot Available
References
Synthesis ReferenceGaudin, K.; Lesellier, E.; Chaminade, P.; Ferrier, D.; Baillet, A.; Tchapla, A. Retention behaviour of ceramides in sub-critical fluid chromatography in comparison with non-aqueous reversed-phase liquid chromatography. Journal of Chromatography, A (2000), 883(1+2), 211-222
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Myher JJ, Kuksis A, Pind S: Molecular species of glycerophospholipids and sphingomyelins of human erythrocytes: improved method of analysis. Lipids. 1989 May;24(5):396-407. [PubMed:2755317 ]
  2. Munoz-Garcia A, Ro J, Brown JC, Williams JB: Identification of complex mixtures of sphingolipids in the stratum corneum by reversed-phase high-performance liquid chromatography and atmospheric pressure photospray ionization mass spectrometry. J Chromatogr A. 2006 Nov 10;1133(1-2):58-68. Epub 2006 Oct 5. [PubMed:17027012 ]
  3. Kuksis A, Myher JJ, Geher K: Quantitation of plasma lipids by gas-liquid chromatography on high temperature polarizable capillary columns. J Lipid Res. 1993 Jun;34(6):1029-38. [PubMed:8354950 ]
  4. Bowser PA, Gray GM: Sphingomyelinase in pig and human epidermis. J Invest Dermatol. 1978 Jun;70(6):331-5. [PubMed:25935 ]
  5. 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. [PubMed:14998372 ]

Only showing the first 10 proteins. There are 66 proteins in total.

Enzymes

General function:
Involved in galactosylceramidase activity
Specific function:
Hydrolyzes the galactose ester bonds of galactosylceramide, galactosylsphingosine, lactosylceramide, and monogalactosyldiglyceride. Enzyme with very low activity responsible for the lysosomal catabolism of galactosylceramide, a major lipid in myelin, kidney and epithelial cells of small intestine and colon.
Gene Name:
GALC
Uniprot ID:
P54803
Molecular weight:
77062.86
General function:
Involved in transferase activity, transferring hexosyl groups
Specific function:
Catalyzes the formation of some glycolipid via the addition of N-acetylgalactosamine (GalNAc) in alpha-1,3-linkage to some substrate. Glycolipids probably serve for adherence of some pathogens
Gene Name:
GBGT1
Uniprot ID:
Q8N5D6
Molecular weight:
40126.9
General function:
Involved in N-acetylglucosaminylphosphatidylinositol de
Specific function:
Involved in the second step of GPI biosynthesis. De-N-acetylation of N-acetylglucosaminyl-phosphatidylinositol.
Gene Name:
PIGL
Uniprot ID:
Q9Y2B2
Molecular weight:
28530.965
General function:
Involved in catalytic activity
Specific function:
Bidirectional lipid cholinephosphotransferase capable of converting phosphatidylcholine (PC) and ceramide to sphingomyelin (SM) and diacylglycerol (DAG) and vice versa. Direction is dependent on the relative concentrations of DAG and ceramide as phosphocholine acceptors. Directly and specifically recognizes the choline head group on the substrate. Also requires two fatty chains on the choline-P donor molecule in order to be recognized efficiently as a substrate. Does not function strictly as a SM synthase. Required for cell growth
Gene Name:
SGMS2
Uniprot ID:
Q8NHU3
Molecular weight:
42279.8
General function:
Involved in catalytic activity
Specific function:
Bidirectional lipid cholinephosphotransferase capable of converting phosphatidylcholine (PC) and ceramide to sphingomyelin (SM) and diacylglycerol (DAG) and vice versa. Direction is dependent on the relative concentrations of DAG and ceramide as phosphocholine acceptors. Directly and specifically recognizes the choline head group on the substrate. Also requires two fatty chains on the choline-P donor molecule in order to be recognized efficiently as a substrate. Does not function strictly as a SM synthase. Suppresses BAX-mediated apoptosis and also prevents cell death in response to stimuli such as hydrogen peroxide, osmotic stress, elevated temperature and exogenously supplied sphingolipids. May protect against cell death by reversing the stress-inducible increase in levels of proapoptotic ceramide. Required for cell growth
Gene Name:
SGMS1
Uniprot ID:
Q86VZ5
Molecular weight:
49207.3
General function:
Involved in hydrolase activity
Specific function:
Converts sphingomyelin to ceramide. Also has phospholipase C activities toward 1,2-diacylglycerolphosphocholine and 1,2-diacylglycerolphosphoglycerol. Isoform 2 and isoform 3 have lost catalytic activity.
Gene Name:
SMPD1
Uniprot ID:
P17405
Molecular weight:
69935.53
General function:
Cell wall/membrane/envelope biogenesis
Specific function:
Catalyzes the first glycosylation step in glycosphingolipid biosynthesis, the transfer of glucose to ceramide. May also serve as a "flippase".
Gene Name:
UGCG
Uniprot ID:
Q16739
Molecular weight:
44853.255
General function:
Involved in phosphatidylinositol N-acetylglucosaminyltransferase activity
Specific function:
Part of the complex catalyzing the transfer of N-acetylglucosamine from UDP-N-acetylglucosamine to phosphatidylinositol, the first step of GPI biosynthesis.
Gene Name:
PIGQ
Uniprot ID:
Q9BRB3
Molecular weight:
65343.25
General function:
Involved in biosynthetic process
Specific function:
Necessary for the synthesis of N-acetylglucosaminyl-phosphatidylinositol, the very early intermediate in GPI-anchor biosynthesis.
Gene Name:
PIGA
Uniprot ID:
P37287
Molecular weight:
54126.065
General function:
Involved in phosphatidylinositol N-acetylglucosaminyltr
Specific function:
Part of the complex catalyzing the transfer of N-acetylglucosamine from UDP-N-acetylglucosamine to phosphatidylinositol, the first step of GPI biosynthesis.
Gene Name:
PIGH
Uniprot ID:
Q14442
Molecular weight:
21080.415

Only showing the first 10 proteins. There are 66 proteins in total.