Human Metabolome Database: Showing metabocard for SM(d18:1/16:0) (HMDB0010169)

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Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References enzymes (52) Show 52 proteins XML

enzymes (52) Show 52 proteins

Record Information

Version

4.0

Status

Detected and Quantified

Creation Date

2008-09-12 02:06:15 UTC

Update Date

2019-12-18 17:20:23 UTC

HMDB ID

HMDB0010169

Secondary Accession Numbers

HMDB0012098
HMDB0061712
HMDB10169
HMDB12098
HMDB61712

Metabolite Identification

Common Name

SM(d18:1/16:0)

Description

Sphingomyelin (d18:1/16:0) or SM(d18:1/16:0) 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(d18:1/16:0) consists of a sphingosine backbone and a palmitic 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

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
(2S,3R,4E)-2-(Palmitoylamino)-3-hydroxyoctadec-4-en-1-yl 2-(trimethylazaniumyl)ethyl phosphate	ChEBI
(2S,3R,4E)-3-Hydroxy-2-(palmitoylamino)octadec-4-en-1-yl 2-(trimethylazaniumyl)ethyl phosphate	ChEBI
C16 Sphingomyelin	ChEBI
C16-Sphingomyelin	ChEBI
Hexadecanoyl sphingomyelin	ChEBI
N-(Hexadecanoyl)-sphing-4-enine-1-phosphocholine	ChEBI
N-Hexadecanoylsphing-4-enine-1-phosphocholine	ChEBI
N-Hexadecanoylsphingomyelin	ChEBI
N-Palmitoyl-D-erythro-sphingosylphosphorylcholine	ChEBI
N-Palmitoylsphing-4-enine-1-phosphocholine	ChEBI
N-Palmitoylsphingomyelin	ChEBI
N-Palmitoylsphingosine-1-phosphocholine	ChEBI
Palmitoyl sphingomyelin (D18:1/16:0)	ChEBI
Palmitoylsphingomyelin	ChEBI
SM(18:1/16:0)	ChEBI
SM(D18:1/16:0)	ChEBI
Sphingomyelin (D18:1/16:0)	ChEBI
Sphingomyelin D18:1/16:0	ChEBI
Sphingomyelin(D18:1/16:0)	ChEBI
(2S,3R,4E)-2-(Palmitoylamino)-3-hydroxyoctadec-4-en-1-yl 2-(trimethylazaniumyl)ethyl phosphoric acid	Generator
(2S,3R,4E)-3-Hydroxy-2-(palmitoylamino)octadec-4-en-1-yl 2-(trimethylazaniumyl)ethyl phosphoric acid	Generator
Palmitoyl sphingomyelin	ChEBI
N-Palmitoylsphingosine-phosphorylcholine	MeSH
N-PSPC	MeSH
N-Palmitoyl-D-erythrosphingosylphosphorylcholine	HMDB
N-Palmitoyl-D-sphingomyelin	HMDB
N-Palmitoylsphingosylphosphorylcholine	HMDB
Sphingomyelin (d18:1 C16:0)	HMDB
Sphingomyelin (dC18:1/C16:0)	HMDB
Sphingomyelin 16:0	HMDB

Chemical Formula

C₃₉H₇₉N₂O₆P

Average Molecular Weight

703.0281

Monoisotopic Molecular Weight

702.567574782

IUPAC Name

(2-{[(2S,3R,4E)-2-hexadecanamido-3-hydroxyoctadec-4-en-1-yl phosphono]oxy}ethyl)trimethylazanium

Traditional Name

(2-{[(2S,3R,4E)-2-hexadecanamido-3-hydroxyoctadec-4-en-1-yl phosphono]oxy}ethyl)trimethylazanium

CAS Registry Number

6254-89-3

SMILES

[H][C@@](COP([O-])(=O)OCC[N+](C)(C)C)(NC(=O)CCCCCCCCCCCCCCC)[C@H](O)\C=C\CCCCCCCCCCCCC

InChI Identifier

InChI=1S/C39H79N2O6P/c1-6-8-10-12-14-16-18-20-22-24-26-28-30-32-38(42)37(36-47-48(44,45)46-35-34-41(3,4)5)40-39(43)33-31-29-27-25-23-21-19-17-15-13-11-9-7-2/h30,32,37-38,42H,6-29,31,33-36H2,1-5H3,(H-,40,43,44,45)/b32-30+/t37-,38+/m0/s1

InChI Key

RWKUXQNLWDTSLO-GWQJGLRPSA-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.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Sphingolipids

Sub Class

Phosphosphingolipids

Direct Parent

Phosphosphingolipids

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 Framework

Aliphatic acyclic compounds

External Descriptors

sphingomyelin d18:1 (CHEBI:78646 )
sphingomyelin 34:1 (CHEBI:78646 )
Ceramide phosphocholines (sphingomyelins) (LMSP03010003 )

Ontology

Physiological effect

Organoleptic effect:

Touch:

Smooth

Disposition

Route of exposure:

Enteral:

Ingestion

Source:

Biological:

Animal

Biological location:

Process

Naturally occurring process:

Biological process:

Chemical reaction:

Lipid peroxidation

Industrial application:

Food and nutrition:

Biological role:

Physical Properties

State

Solid

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
Water Solubility	5.3e-05 g/L	ALOGPS
logP	5.12	ALOGPS
logP	6.98	ChemAxon
logS	-7.4	ALOGPS
pKa (Strongest Acidic)	1.87	ChemAxon
pKa (Strongest Basic)	-1.1	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	107.92 Å²	ChemAxon
Rotatable Bond Count	36	ChemAxon
Refractivity	213.94 m³·mol⁻¹	ChemAxon
Polarizability	88.76 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	0	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Spectra

Not Available

Biological Properties

Cellular Locations

Extracellular
Membrane

Biospecimen Locations

Blood
Cerebrospinal Fluid (CSF)
Feces
Saliva
Urine

Tissue Locations

All Tissues

Pathways

Not Available

Name	SMPDB/Pathwhiz	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected and Quantified	60.00-190.0 uM	Adult (>18 years old)	Both	Normal	Molecular You	details
Blood	Detected and Quantified	69.9 (61-79.4) uM	Newborn (0-30 days old)	Not Available	Normal	25754623	details
Blood	Detected and Quantified	121 (101-139) uM	Infant (0-1 year old)	Not Available	Normal	25754623	details
Blood	Detected and Quantified	81 +/- 0.9 uM	Adult (>18 years old)	Both	Normal	20671299	details
Blood	Detected and Quantified	114.4 +/- 19.7 uM	Adult (>18 years old)	Both	Normal	28278231	details
Cerebrospinal Fluid (CSF)	Detected and Quantified	0.336 +/- 0.109 uM	Adult (>18 years old)	Not Specified	Normal	22546835	details
Feces	Detected but not Quantified		Adult (>18 years old)	Both	Normal	29808030	details
Feces	Detected but not Quantified		Adult (>18 years old)	Both	Normal	27543620	details
Feces	Detected but not Quantified		Adult (>18 years old)	Both	Normal	25037050	details
Saliva	Detected and Quantified	0.282 +/- 0.145 uM	Adult (>18 years old)	Both	Normal	Zerihun T. Dame, ...	details
Urine	Detected and Quantified	8.92 +/- 0.59 umol/mmol creatinine	Adolescent (13-18 years old)	Both	Normal	26910390	details
Urine	Detected and Quantified	0.01 (0.0016-0.07) umol/mmol creatinine	Adult (>18 years old)	Both	Normal	24023812	details
Urine	Detected and Quantified	0.0203 +/- 0.0374 umol/mmol creatinine	Children (1 - 13 years old)	Not Specified	Normal	Mordechai, Hien, ...	details

Abnormal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected and Quantified	79.1 +/- 20.6 uM	Children (1-13 years old)	Both	Obesity	Metabolomics reve...	details
Blood	Detected and Quantified	86.1 +/- 23.2 uM	Children (1-13 years old)	Both	Obesity	Metabolomics reve...	details
Feces	Detected but not Quantified		Newborn (0-30 days old)	Not Specified	Premature neonates	23210743	details
Feces	Detected but not Quantified		Adult (>18 years old)	Both	Colorectal Cancer	25037050	details
Urine	Detected and Quantified	6.94 +/- 0.42 umol/mmol creatinine	Adolescent (13-18 years old)	Both	Obese	26910390	details
Urine	Detected and Quantified	0.0194 +/- 0.0383 umol/mmol creatinine	Children (1 - 13 years old)	Not Specified	Eosinophilic esophagitis	Mordechai, Hien, ...	details
Urine	Detected and Quantified	0.0218 +/- 0.0369 umol/mmol creatinine	Children (1 - 13 years old)	Not Specified	Gastroesophageal reflux disease	Mordechai, Hien, ...	details

Associated Disorders and Diseases

Disease References

Colorectal cancer
Goedert JJ, Sampson JN, Moore SC, Xiao Q, Xiong X, Hayes RB, Ahn J, Shi J, Sinha R: Fecal metabolomics: assay performance and association with colorectal cancer. Carcinogenesis. 2014 Sep;35(9):2089-96. doi: 10.1093/carcin/bgu131. Epub 2014 Jul 18. [PubMed:25037050 ]
Eosinophilic esophagitis
(). Mordechai, Hien, and David S. Wishart. .
Obesity
Cho K, Moon JS, Kang JH, Jang HB, Lee HJ, Park SI, Yu KS, Cho JY: Combined untargeted and targeted metabolomic profiling reveals urinary biomarkers for discriminating obese from normal-weight adolescents. Pediatr Obes. 2017 Apr;12(2):93-101. doi: 10.1111/ijpo.12114. Epub 2016 Feb 22. [PubMed:26910390 ] 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.

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)
601665 (Obesity)

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB027352

KNApSAcK ID

Not Available

Chemspider ID

8115562

KEGG Compound ID

Not Available

BioCyc ID

CPD66-42

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

9939941

PDB ID

Not Available

ChEBI ID

78646

Food Biomarker Ontology

Not Available

VMH ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Divecha N, Irvine RF: Phospholipid signaling. Cell. 1995 Jan 27;80(2):269-78. [PubMed:7834746 ]
Hannun YA: The sphingomyelin cycle and the second messenger function of ceramide. J Biol Chem. 1994 Feb 4;269(5):3125-8. [PubMed:8106344 ]
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 ]
Simons K, Toomre D: Lipid rafts and signal transduction. Nat Rev Mol Cell Biol. 2000 Oct;1(1):31-9. [PubMed:11413487 ]
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 ]
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 ]
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 ]
de Jong A, Cheng TY, Huang S, Gras S, Birkinshaw RW, Kasmar AG, Van Rhijn I, Pena-Cruz V, Ruan DT, Altman JD, Rossjohn J, Moody DB: CD1a-autoreactive T cells recognize natural skin oils that function as headless antigens. Nat Immunol. 2014 Feb;15(2):177-85. doi: 10.1038/ni.2790. Epub 2013 Dec 22. [PubMed:24362891 ]
Cevc, Gregor (1993). Phospholipids Handbook. Marcel Dekker.
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.

Show all enzymes and transporters

Enzymes

Enzyme Details

1. Globoside alpha-1,3-N-acetylgalactosaminyltransferase 1

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

Enzyme Details

2. N-acetylglucosaminyl-phosphatidylinositol de-N-acetylase

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

Enzyme Details

3. Phosphatidylcholine:ceramide cholinephosphotransferase 2

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

Enzyme Details

4. Phosphatidylcholine:ceramide cholinephosphotransferase 1

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

Enzyme Details

5. Sphingomyelin phosphodiesterase

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

Enzyme Details

6. Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 1

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

Enzyme Details

7. Phosphatidylinositol N-acetylglucosaminyltransferase subunit Q

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

Enzyme Details

8. Phosphatidylinositol N-acetylglucosaminyltransferase subunit A

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

Enzyme Details

9. Phosphatidylinositol N-acetylglucosaminyltransferase subunit H

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

Enzyme Details

10. Phosphatidylinositol N-acetylglucosaminyltransferase subunit P

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.

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Showing metabocard for SM(d18:1/16:0) (HMDB0010169)

Structure for HMDB0010169 (SM(d18:1/16:0))

Enzymes