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Record Information
Version4.0
StatusDetected and Quantified
Creation Date2009-02-19 23:38:54 UTC
Update Date2020-06-10 18:22:06 UTC
HMDB IDHMDB0011697
Secondary Accession Numbers
  • HMDB0012106
  • HMDB11697
  • HMDB12106
Metabolite Identification
Common NameSM(d18:1/24:0)
DescriptionSphingomyelin (d18:1/24:0) or SM(d18:1/24:0) is a type of sphingolipid found in animal cell membranes, especially in the membranous myelin sheath which surrounds some nerve cell axons. It usually consists of phosphorylcholine and ceramide. SM(d18:1/24:0) consists of a sphingosine backbone and a lignoceric acid chain. In humans, sphingomyelin is the only membrane phospholipid not derived from glycerol. Like all sphingolipids, SM has a ceramide core (sphingosine bonded to a fatty acid via an amide linkage). In addition, it contains one polar head group, which is either phosphocholine or phosphoethanolamine. The plasma membrane of cells is highly enriched in sphingomyelin and is considered largely to be found in the exoplasmic leaflet of the cell membrane. However, there is some evidence that there may also be a sphingomyelin pool in the inner leaflet of the membrane. Moreover, neutral sphingomyelinase-2, an enzyme that breaks down sphingomyelin into ceramide, has been found to localize exclusively to the inner leaflet further suggesting that there may be sphingomyelin present there. Sphingomyelin can accumulate in a rare hereditary disease called Niemann-Pick Disease, types A and B. Niemann-Pick disease is a genetically-inherited disease caused by a deficiency in the enzyme sphingomyelinase, which causes the accumulation of sphingomyelin in spleen, liver, lungs, bone marrow, and the brain, causing irreversible neurological damage. SMs play a role in signal transduction. Sphingomyelins are synthesized by the transfer of phosphorylcholine from phosphatidylcholine to a ceramide in a reaction catalyzed by sphingomyelin synthase.
Structure
Data?1591813326
Synonyms
ValueSource
(2S,3R,4E)-3-Hydroxy-2-(tetracosanoylamino)octadec-4-en-1-yl 2-(trimethylammonio)ethyl phosphateChEBI
C24 SphingomyelinChEBI
N-(Tetracosanoyl)-sphing-4-enine-1-phosphocholineChEBI
N-Lignoceroylsphing-4-enine-1-phosphocholineChEBI
N-Tetracosanoylsphing-4-enine-1-phosphocholineChEBI
N-Tetracosanoylsphingosine-1-phosphocholineChEBI
SM(d18:1/24:0)ChEBI
SPH(d18:1/24:0)ChEBI
Sphingomyelin (d18:1/24:0)ChEBI
(2S,3R,4E)-3-Hydroxy-2-(tetracosanoylamino)octadec-4-en-1-yl 2-(trimethylammonio)ethyl phosphoric acidGenerator
24:0 SphingomyelinHMDB
C24-SphingomyelinHMDB
Lignoceroyl sphingomyelinHMDB
SM d18:1/24:0HMDB
Sphingomyelin (d18:1,C24:0)HMDB
Sphingomyelin C24:0HMDB
Chemical FormulaC47H95N2O6P
Average Molecular Weight815.259
Monoisotopic Molecular Weight814.692775785
IUPAC Name(2-{[(2S,3R,4E)-3-hydroxy-2-tetracosanamidooctadec-4-en-1-yl phosphono]oxy}ethyl)trimethylazanium
Traditional Name(2-{[(2S,3R,4E)-3-hydroxy-2-tetracosanamidooctadec-4-en-1-yl phosphono]oxy}ethyl)trimethylazanium
CAS Registry Number60037-60-7
SMILES
[H][C@@](COP([O-])(=O)OCC[N+](C)(C)C)(NC(=O)CCCCCCCCCCCCCCCCCCCCCCC)[C@H](O)\C=C\CCCCCCCCCCCCC
InChI Identifier
InChI=1S/C47H95N2O6P/c1-6-8-10-12-14-16-18-20-21-22-23-24-25-26-27-29-31-33-35-37-39-41-47(51)48-45(44-55-56(52,53)54-43-42-49(3,4)5)46(50)40-38-36-34-32-30-28-19-17-15-13-11-9-7-2/h38,40,45-46,50H,6-37,39,41-44H2,1-5H3,(H-,48,51,52,53)/b40-38+/t45-,46+/m0/s1
InChI KeyQEDPUVGSSDPBMD-XTAIVQBESA-N
Chemical Taxonomy
Description belongs to the class of organic compounds known as phosphosphingolipids. These are sphingolipids with a structure based on a sphingoid base that is attached to a phosphate head group. They differ from phosphonospingolipids which have a phosphonate head group.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassSphingolipids
Sub ClassPhosphosphingolipids
Direct ParentPhosphosphingolipids
Alternative Parents
Substituents
  • Sphingoid-1-phosphate or derivatives
  • Phosphocholine
  • Phosphoethanolamine
  • Dialkyl phosphate
  • Fatty amide
  • N-acyl-amine
  • Organic phosphoric acid derivative
  • Phosphoric acid ester
  • Fatty acyl
  • Alkyl phosphate
  • Tetraalkylammonium salt
  • Quaternary ammonium salt
  • Secondary carboxylic acid amide
  • Secondary alcohol
  • Carboxamide group
  • Carboxylic acid derivative
  • Organic zwitterion
  • Alcohol
  • Organic oxide
  • Organooxygen compound
  • Organonitrogen compound
  • Organopnictogen compound
  • Organic oxygen compound
  • Organic nitrogen compound
  • Hydrocarbon derivative
  • Carbonyl group
  • Amine
  • Organic salt
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological 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 Solubility3.2e-05 g/LALOGPS
logP6.3ALOGPS
logP10.53ChemAxon
logS-7.5ALOGPS
pKa (Strongest Acidic)1.87ChemAxon
pKa (Strongest Basic)-1.1ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area107.92 ŲChemAxon
Rotatable Bond Count44ChemAxon
Refractivity250.75 m³·mol⁻¹ChemAxon
Polarizability105.97 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Spectra
Not Available
Biological Properties
Cellular Locations
  • Extracellular
  • Membrane
Biospecimen Locations
  • Blood
  • Cerebrospinal Fluid (CSF)
  • Saliva
  • Urine
Tissue Locations
  • All Tissues
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified11.0-39.0 uMAdult (>18 years old)Both
Normal
details
BloodDetected and Quantified14.4 (12.1-16.6) uMNewborn (0-30 days old)Not Available
Normal
details
BloodDetected and Quantified19.3 (16.2-23.5) uMInfant (0-1 year old)Not Available
Normal
details
BloodDetected and Quantified12.5 +/- 0.6 uMAdult (>18 years old)BothNormal details
BloodDetected and Quantified22.0 +/- 4.73 uMAdult (>18 years old)BothNormal details
Cerebrospinal Fluid (CSF)Detected and Quantified0.114 +/- 0.022 uMAdult (>18 years old)Not SpecifiedNormal details
SalivaDetected and Quantified0.222 +/- 0.090 uMAdult (>18 years old)BothNormal
    • Zerihun T. Dame, ...
details
UrineDetected and Quantified0.0085 (0.0047-0.02) umol/mmol creatinineAdult (>18 years old)Both
Normal
details
UrineDetected and Quantified0.032 +/- 0.0606 umol/mmol creatinineChildren (1 - 13 years old)Not Specified
Normal
    • Mordechai, Hien, ...
details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified17.5 +/- 5.2 uMChildren (1-13 years old)Both
Obesity
    • Metabolomics reve...
details
BloodDetected and Quantified19.6 +/- 6.4 uMChildren (1-13 years old)Both
Obesity
    • Metabolomics reve...
details
UrineDetected and Quantified0.0157 +/- 0.0069 umol/mmol creatinineChildren (1 - 13 years old)Not Specified
Eosinophilic esophagitis
    • Mordechai, Hien, ...
details
UrineDetected and Quantified0.019 +/- 0.0129 umol/mmol creatinineChildren (1 - 13 years old)Not Specified
Gastroesophageal reflux disease
    • Mordechai, Hien, ...
details
Associated Disorders and Diseases
Disease References
Obesity
  1. Simone Wahl, Christina Holzapfel, Zhonghao Yu, Michaela Breier, Ivan Kondofersky, Christiane Fuchs, Paula Singmann, Cornelia Prehn, Jerzy Adamski, Harald Grallert, Thomas Illig, Rui Wang-Sattler, Thomas Reinehr (2013). Metabolomics reveals determinants of weight loss during lifestyle intervention in obese children. Metabolomics.
Eosinophilic esophagitis
  1. (). Mordechai, Hien, and David S. Wishart. .
Associated OMIM IDs
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID24846875
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound44260127
PDB IDNot Available
ChEBI ID83360
Food Biomarker OntologyNot Available
VMH IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Ding J, Sorensen CM, Jaitly N, Jiang H, Orton DJ, Monroe ME, Moore RJ, Smith RD, Metz TO: Application of the accurate mass and time tag approach in studies of the human blood lipidome. J Chromatogr B Analyt Technol Biomed Life Sci. 2008 Aug 15;871(2):243-52. doi: 10.1016/j.jchromb.2008.04.040. Epub 2008 May 7. [PubMed:18502191 ]
  2. Divecha N, Irvine RF: Phospholipid signaling. Cell. 1995 Jan 27;80(2):269-78. [PubMed:7834746 ]
  3. Hannun YA: The sphingomyelin cycle and the second messenger function of ceramide. J Biol Chem. 1994 Feb 4;269(5):3125-8. [PubMed:8106344 ]
  4. Ghosh S, Strum JC, Bell RM: Lipid biochemistry: functions of glycerolipids and sphingolipids in cellular signaling. FASEB J. 1997 Jan;11(1):45-50. [PubMed:9034165 ]
  5. Simons K, Toomre D: Lipid rafts and signal transduction. Nat Rev Mol Cell Biol. 2000 Oct;1(1):31-9. [PubMed:11413487 ]
  6. Watson AD: Thematic review series: systems biology approaches to metabolic and cardiovascular disorders. Lipidomics: a global approach to lipid analysis in biological systems. J Lipid Res. 2006 Oct;47(10):2101-11. Epub 2006 Aug 10. [PubMed:16902246 ]
  7. Sethi JK, Vidal-Puig AJ: Thematic review series: adipocyte biology. Adipose tissue function and plasticity orchestrate nutritional adaptation. J Lipid Res. 2007 Jun;48(6):1253-62. Epub 2007 Mar 20. [PubMed:17374880 ]
  8. Lingwood D, Simons K: Lipid rafts as a membrane-organizing principle. Science. 2010 Jan 1;327(5961):46-50. doi: 10.1126/science.1174621. [PubMed:20044567 ]
  9. Cevc, Gregor (1993). Phospholipids Handbook. Marcel Dekker.
  10. Gunstone, Frank D., John L. Harwood, and Albert J. Dijkstra (2007). The lipid handbook with CD-ROM. CRC Press.

Only showing the first 10 proteins. There are 50 proteins in total.

Enzymes

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 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:
Involved in galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase activity
Specific function:
Involved in the biosynthesis of L2/HNK-1 carbohydrate epitope on glycoproteins. Can also play a role in glycosaminoglycan biosynthesis. Substrates include asialo-orosomucoid (ASOR), asialo-fetuin, and asialo-neural cell adhesion molecule. Requires sphingomyelin for activity: stearoyl-sphingomyelin was the most effective, followed by palmitoyl-sphingomyelin and lignoceroyl-sphingomyelin. Activity was demonstrated only for sphingomyelin with a saturated fatty acid and not for that with an unsaturated fatty acid, regardless of the length of the acyl group (By similarity).
Gene Name:
B3GAT1
Uniprot ID:
Q9P2W7
Molecular weight:
38255.675
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
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:
PIGP
Uniprot ID:
P57054
Molecular weight:
18089.055
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:
PIGC
Uniprot ID:
Q92535
Molecular weight:
33582.18
General function:
Involved in catalytic activity
Specific function:
Converts sphingomyelin to ceramide. Also has phospholipase C activity toward palmitoyl lyso-phosphocholine. Does not appear to have nucleotide pyrophosphatase activity.
Gene Name:
ENPP7
Uniprot ID:
Q6UWV6
Molecular weight:
51493.415

Only showing the first 10 proteins. There are 50 proteins in total.