Bovine Metabolome Database: Showing metabocard for Ceramide (d18:1/24:0) (BMDB0004956)

Identification Taxonomy Physical properties Pathways Spectra Concentrations Links References enzymes (4) Show 4 proteins XML

Record Information

Version

1.0

Creation Date

2016-09-30 23:13:44 UTC

Update Date

2020-05-11 20:57:25 UTC

BMDB ID

BMDB0004956

Secondary Accession Numbers

BMDB04956

Metabolite Identification

Common Name

Ceramide (d18:1/24:0)

Description

Ceramide (d18:1/24:0), also known as C24 cer or N-(tetracosanoyl)ceramide, 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. Thus, ceramide (D18:1/24:0) is considered to be a ceramide lipid molecule. Ceramide (d18:1/24:0) is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral.

Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
C24 Cer	ChEBI
Cer(d18:1/24:0)	ChEBI
N-(Tetracosanoyl)-sphing-4-enine	ChEBI
N-(Tetracosanoyl)ceramide	ChEBI
N-(Tetracosanoyl)sphing-4-enine	ChEBI
N-Lignoceroylsphingosine	ChEBI
N-Tetracosanoylsphing-4-enine	ChEBI
(2S,3R,4E)-2-acylamino-1,3-Octadec-4-enediol	HMDB
(2S,3R,4E)-2-Acylaminooctadec-4-ene-1,3-diol	HMDB
Cer	HMDB
Ceramide	HMDB
N-Acylsphingosine	HMDB
N-[(1S,2R,3E)-2-Hydroxy-1-(hydroxymethyl)-3-heptadecenyl]-octadecanamide	HMDB
Ceramide (d18:1/24:0)	ChEBI
C24-Ceramide	HMDB
C24:0 Ceramide	HMDB
Cer d18:1/24:0	HMDB
Ceramide (d18:1,C24:0)	HMDB
Ceramide 24	HMDB
Ceramide d18:1/24:0	HMDB
Ceramide(d18:1/24:0)	HMDB
D-erythro-1,3-Dihydroxy-2-tetracosanoylamido-trans-4-octadecene	HMDB
N-Tetracosanoyl C18-sphingosine	HMDB

Chemical Formula

C₄₂H₈₃NO₃

Average Molecular Weight

650.1133

Monoisotopic Molecular Weight

649.637295527

IUPAC Name

N-[(2S,3R,4E)-1,3-dihydroxyoctadec-4-en-2-yl]tetracosanamide

Traditional Name

C24 cer

CAS Registry Number

104404-17-3

SMILES

CCCCCCCCCCCCCCCCCCCCCCCC(=O)N[C@@H](CO)[C@H](O)\C=C\CCCCCCCCCCCCC

InChI Identifier

InChI=1S/C42H83NO3/c1-3-5-7-9-11-13-15-17-18-19-20-21-22-23-24-26-28-30-32-34-36-38-42(46)43-40(39-44)41(45)37-35-33-31-29-27-25-16-14-12-10-8-6-4-2/h35,37,40-41,44-45H,3-34,36,38-39H2,1-2H3,(H,43,46)/b37-35+/t40-,41+/m0/s1

InChI Key

ZJVVOYPTFQEGPH-AUTSUKAISA-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.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Sphingolipids

Sub Class

Ceramides

Direct Parent

Ceramides

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 Framework

Aliphatic acyclic compounds

External Descriptors

N-acylsphingosine (CHEBI:72965 )
N-acylsphingosines (ceramides) (LMSP02010012 )

Ontology

Status

Expected but not Quantified

Origin

Endogenous

Exogenous

Biofunction

Not Available

Application

Not Available

Cellular locations

Cell membrane
Cytoplasm
Endosome
Intracellular membrane
Membrane
Mitochondria
Myelin sheath

Physical Properties

State

Solid

Experimental Properties

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

Predicted Properties

Property	Value	Source
logP	10.35	ALOGPS
logP	14.42	ChemAxon
logS	-7.5	ALOGPS
pKa (Strongest Acidic)	13.62	ChemAxon
pKa (Strongest Basic)	-1	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	69.56 Å²	ChemAxon
Rotatable Bond Count	38	ChemAxon
Refractivity	202.58 m³·mol⁻¹	ChemAxon
Polarizability	90.32 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Spectra

Spectrum Type	Description	Splash Key
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0udi-0000009000-a65c953744cc2d2e8548	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0w29-0050009000-945984dc47ce37d19ab7	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-01q9-0090006000-a840c8942258f6ac9cdb	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0a4i-0000009000-c5cb4fa38a3177776a50	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0a4i-0000009000-c5cb4fa38a3177776a50	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-000i-0000009000-28eaa8cbf7f8fc05a030	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0002-0000009000-1291f1515f82f39bf015	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0002-0010009000-718b412287d72ba417df	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-00kb-0022009000-9b9ac10481ff90fda17f	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0udi-0000009000-13ac87f42e4669f45e03	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0w29-0050009000-c0fb077679d68208f7ea	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-01q9-0090006000-701b761eeb9ec4018cdf	View in MoNA

Biological Properties

Cellular Locations

Cell membrane
Cytoplasm
Endosome
Intracellular membrane
Membrane
Mitochondria
Myelin sheath

Biospecimen Locations

Brain
Epidermis
Fibroblasts
Intestine
Kidney
Liver
Neuron
Pancreas
Placenta
Platelet
Skeletal Muscle
Spleen
Testis
Thyroid Gland

Pathways

Not Available

Name	SMPDB/Pathwhiz	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Brain	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Epidermis	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Fibroblasts	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Intestine	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Kidney	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Liver	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Neuron	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Pancreas	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Placenta	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Platelet	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Skeletal Muscle	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Spleen	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Testis	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Thyroid Gland	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details

Abnormal Concentrations

Not Available

External Links

HMDB ID

HMDB0004956

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB023543

KNApSAcK ID

Not Available

Chemspider ID

4446684

KEGG Compound ID

C00195

BioCyc ID

CERAMIDE

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

7209

PubChem Compound

5283571

PDB ID

Not Available

ChEBI ID

72965

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Not Available

Enzymes

Enzyme Details

1. Acid ceramidase

General function:: Involved in ceramidase activity
Specific function:: Lysosomal ceramidase that hydrolyzes sphingolipid ceramides into sphingosine and free fatty acids at acidic pH (By similarity). Ceramides, sphingosine, and its phosphorylated form sphingosine-1-phosphate are bioactive lipids that mediate cellular signaling pathways regulating several biological processes including cell proliferation, apoptosis and differentiation (By similarity). Has a higher catalytic efficiency towards C12-ceramides versus other ceramides (By similarity). Also catalyzes the reverse reaction allowing the synthesis of ceramides from fatty acids and sphingosine (By similarity). For the reverse synthetic reaction, the natural sphingosine D-erythro isomer is more efficiently utilized as a substrate compared to D-erythro-dihydrosphingosine and D-erythro-phytosphingosine, while the fatty acids with chain lengths of 12 or 14 carbons are the most efficiently used (By similarity). Has also an N-acylethanolamine hydrolase activity (By similarity). By regulating the levels of ceramides, sphingosine and sphingosine-1-phosphate in the epidermis, mediates the calcium-induced differentiation of epidermal keratinocytes (By similarity). Also indirectly regulates tumor necrosis factor/TNF-induced apoptosis (By similarity). By regulating the intracellular balance between ceramides and sphingosine, in adrenocortical cells, probably also acts as a regulator of steroidogenesis (By similarity).
Gene Name:: ASAH1
Uniprot ID:: Q17QB3
Molecular weight:: 44965.0

Enzyme Details

2. Sphingomyelin phosphodiesterase

General function:: Involved in hydrolase activity, acting on glycosyl bonds
Specific function:: Converts sphingomyelin to ceramide. Also has phospholipase C activities toward 1,2-diacylglycerolphosphocholine and 1,2-diacylglycerolphosphoglycerol.
Gene Name:: SMPD1
Uniprot ID:: Q0VD19
Molecular weight:: 69392.0

Enzyme Details

3. Lysosomal acid glucosylceramidase

General function:: Involved in cation binding
Specific function:: Glucosylceramidase that catalyzes, within the lysosomal compartment, the hydrolysis of glucosylceramide/GlcCer into free ceramide and glucose. Thereby, plays a central role in the degradation of complex lipids and the turnover of cellular membranes. Through the production of ceramides, participates to the PKC-activated salvage pathway of ceramide formation. Also plays a role in cholesterol metabolism. May either catalyze the glucosylation of cholesterol, through a transglucosylation reaction that transfers glucose from glucosylceramide to cholesterol. The short chain saturated C8:0-GlcCer and the mono-unsaturated C18:0-GlcCer being the most effective glucose donors for that transglucosylation reaction. Under specific conditions, may alternatively catalyze the reverse reaction, transferring glucose from cholesteryl-beta-D-glucoside to ceramide. Finally, may also hydrolyze cholesteryl-beta-D-glucoside to produce D-glucose and cholesterol.
Gene Name:: GBA
Uniprot ID:: Q2KHZ8
Molecular weight:: 59855.0

Enzyme Details

4. Ceramide transfer protein

General function:: Involved in lipid transport
Specific function:: Shelters ceramides and diacylglycerol lipids inside its START domain and mediates the intracellular trafficking of ceramides and diacylglycerol lipids in a non-vesicular manner.
Gene Name:: CERT1
Uniprot ID:: Q9GKI7
Molecular weight:: 70847.0

Showing metabocard for Ceramide (d18:1/24:0) (BMDB0004956)

Structure for BMDB0004956 (Ceramide (d18:1/24:0))

Enzymes