You are using an unsupported browser. Please upgrade your browser to a newer version to get the best experience on Human Metabolome Database.
Record Information
Version4.0
StatusDetected and Quantified
Creation Date2010-03-24 16:57:27 UTC
Update Date2018-01-13 00:26:32 UTC
HMDB IDHMDB0013469
Secondary Accession Numbers
  • HMDB13469
Metabolite Identification
Common NameSM(d18:0/24:1(15Z)(OH))
DescriptionSphingomyelin (d18:0/24:1(15Z)(OH))or SM(d18:0/24:1(15Z)(OH)) 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. In humans, sphingomyelin is the only membrane phospholipid not derived from glycerol. Like all sphingolipids, SPH 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 localise 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
Thumb
Synonyms
ValueSource
C24:1-OH SphingomyelinChEBI
Hydroxysphingomyeline C24:1ChEBI
N-[(15Z)-3-Hydroxytetracos-15-enoyl]sphing-4-enine-1-phosphocholineChEBI
SM(D18:1/24:1(15Z)(OH))ChEBI
N-(15Z-Tetracosenoyl)-sphing-4-enine-1-phosphocholineHMDB
Chemical FormulaC47H93N2O7P
Average Molecular Weight829.2243
Monoisotopic Molecular Weight828.672039852
IUPAC Name(2-{[(2S,3R,4E)-3-hydroxy-2-[(15Z)-3-hydroxytetracos-15-enamido]octadec-4-en-1-yl phosphonato]oxy}ethyl)trimethylazanium
Traditional Name(2-{[(2S,3R,4E)-3-hydroxy-2-[(15Z)-3-hydroxytetracos-15-enamido]octadec-4-en-1-yl phosphonato]oxy}ethyl)trimethylazanium
CAS Registry NumberNot Available
SMILES
CCCCCCCCCCCCC\C=C\[C@@H](O)[C@H](COP([O-])(=O)OCC[N+](C)(C)C)NC(=O)CC(O)CCCCCCCCCCC\C=C/CCCCCCCC
InChI Identifier
InChI=1S/C47H93N2O7P/c1-6-8-10-12-14-16-18-20-21-22-23-24-25-27-28-30-32-34-36-38-44(50)42-47(52)48-45(43-56-57(53,54)55-41-40-49(3,4)5)46(51)39-37-35-33-31-29-26-19-17-15-13-11-9-7-2/h20-21,37,39,44-46,50-51H,6-19,22-36,38,40-43H2,1-5H3,(H-,48,52,53,54)/b21-20-,39-37+/t44?,45-,46+/m0/s1
InChI KeyIOOMOQUTKQGEFH-BSZNTFKYSA-N
Chemical Taxonomy
DescriptionThis compound 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 DescriptorsNot Available
Ontology
Origin
  • Endogenous
  • Food
Biofunction
  • Cell signaling
  • Energy source
  • Fuel and energy storage
  • Fuel or energy source
  • Membrane component
  • Membrane integrity/stability
Application
  • Nutrients
  • Stabilizers
  • Surfactants and Emulsifiers
Cellular locations
  • Extracellular
  • 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
Water Solubility3.1e-05 g/LALOGPS
logP5.81ALOGPS
logP8.94ChemAxon
logS-7.5ALOGPS
pKa (Strongest Acidic)1.87ChemAxon
pKa (Strongest Basic)-1.2ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area128.15 ŲChemAxon
Rotatable Bond Count43ChemAxon
Refractivity253.38 m³·mol⁻¹ChemAxon
Polarizability104.13 ųChemAxon
Number of Rings0ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash Key
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-01u9-5011109240-f45aa83673aaedd9b0e1View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-003s-1131109100-6ee25eea1e94d73daadbView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-001r-9173002300-42f818b95026245bfd6eView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-004i-0001000490-2592f8fea67f74bbabedView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-00b9-1026103920-ea9f4b2bfa57ca6b4c1bView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0059-7119002000-f70cbc7f0bbf017e71c0View in MoNA
Biological Properties
Cellular Locations
  • Extracellular
  • Membrane
Biofluid Locations
  • Blood
  • Cerebrospinal Fluid (CSF)
  • Saliva
  • Urine
Tissue LocationNot Available
PathwaysNot Available
NameSMPDB/PathwhizKEGG
Normal Concentrations
BiofluidStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified0.84 (0.71-1.06) uMNewborn (0-30 days old)Not Available
Normal
details
BloodDetected and Quantified0.70-3.60 uMAdult (>18 years old)Both
Normal
details
BloodDetected and Quantified1.1 (0.84-1.41) uMInfant (0-1 year old)Not Available
Normal
details
BloodDetected and Quantified57.1 +/- 11.7 uMAdult (>18 years old)BothNormal details
Cerebrospinal Fluid (CSF)Detected and Quantified0.017 +/- 0.004 uMAdult (>18 years old)Not SpecifiedNormal details
SalivaDetected and Quantified0.020 +/- 0.008 uMAdult (>18 years old)BothNormal
    • Zerihun T. Dame, ...
details
UrineDetected and Quantified0.001 (0.00034-0.0025) umol/mmol creatinineAdult (>18 years old)Both
Normal
details
UrineDetected and Quantified0.003 +/- 0.0061 umol/mmol creatinineChildren (1 - 13 years old)Not Specified
Normal
    • Mordechai, Hien, ...
details
Abnormal Concentrations
BiofluidStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified1.04 +/- 0.35 uMChildren (1-13 years old)Both
Obesity
    • Metabolomics reve...
details
BloodDetected and Quantified1.01 +/- 0.33 uMChildren (1-13 years old)Both
Obesity
    • Metabolomics reve...
details
BloodDetected and Quantified1.7359 (0.44) uMAdult (>18 years old)FemalePregnancy details
UrineDetected and Quantified0.0009 +/- 0.0008 umol/mmol creatinineChildren (1 - 13 years old)Not Specified
Eosinophilic esophagitis
    • Mordechai, Hien, ...
details
UrineDetected and Quantified0.0012 +/- 0.0015 umol/mmol creatinineChildren (1 - 13 years old)Not Specified
Gastroesophageal reflux disease
    • Mordechai, Hien, ...
details
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB029469
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDC00550
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkSphingomyelin
METLIN IDNot Available
PubChem Compound53481791
PDB IDNot Available
ChEBI ID90006
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Simons K, Toomre D: Lipid rafts and signal transduction. Nat Rev Mol Cell Biol. 2000 Oct;1(1):31-9. [PubMed:11413487 ]
  2. 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 ]
  3. 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 ]
  4. 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 ]
  5. Divecha N, Irvine RF: Phospholipid signaling. Cell. 1995 Jan 27;80(2):269-78. [PubMed:7834746 ]
  6. 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 ]
  7. Hannun YA: The sphingomyelin cycle and the second messenger function of ceramide. J Biol Chem. 1994 Feb 4;269(5):3125-8. [PubMed:8106344 ]
  8. Cevc, Gregor (1993). Phospholipids Handbook. Marcel Dekker.
  9. 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 52 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 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:
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

Only showing the first 10 proteins. There are 52 proteins in total.