Bovine Metabolome Database: Showing metabocard for Ceramide (d18:1/16:0) (BMDB0004949)

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 23:13:35 UTC

Update Date

2020-05-11 20:57:20 UTC

BMDB ID

BMDB0004949

Secondary Accession Numbers

BMDB04949

Metabolite Identification

Common Name

Ceramide (d18:1/16:0)

Description

Cer(d18:1/16:0), also known as N-hexadecanoyl-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(d18:1/16:0) is a colorless solid that consists of an unsaturated 18-carbon sphingoid base with an attached saturated hexadecanoyl fatty acid side chain. In most mammalian SPs, the 18-carbon sphingoid bases are predominant (PMID: 9759481 ).

Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
(2S,3R,4E)-2-Acylamino-1,3-octadec-4-enediol	ChEBI
(2S,3R,4E)-2-Acylaminooctadec-4-ene-1,3-diol	ChEBI
C16 Cer	ChEBI
C16 Ceramide	ChEBI
C16-0(Palmitoyl)ceramide	ChEBI
Ceramide (D18:1/16:0)	ChEBI
N-(Hexadecanoyl)-sphing-4-enine	ChEBI
N-(Hexadecanoyl)ceramide	ChEBI
N-(Hexadecanoyl)sphing-4-enine	ChEBI
N-(Palmitoyl)ceramide	ChEBI
N-Hexadecanoyl-D-erythro-sphingosine	ChEBI
N-Hexadecanoylsphing-4-enine	ChEBI
N-Palmitoyl-sphingosine	ChEBI
N-Palmitoylsphing-4-enine	ChEBI
N-Palmitoylsphingosine	ChEBI
Cer	HMDB
Ceramide	HMDB
N-Acylsphingosine	HMDB
N-[(1S,2R,3E)-2-Hydroxy-1-(hydroxymethyl)-3-heptadecenyl]-octadecanamide	HMDB
C16-Ceramide	HMDB
NFA(C16)cer	HMDB
Palmitoylceramide	HMDB
C(16)-Ceramide	HMDB
N-Palmitoylsphingosine, (r,s-(e))-(+-)	HMDB
C16-Palmitoylceramide	HMDB
N-Palmitoylsphingosine, R-(r,s-(e))	HMDB
PCer CPD	HMDB
Ceramide-C16	HMDB
(2S,3R,4E)-2-N-Palmitoyloctadecasphinga-4-ene	HMDB
C16:0-Ceramide	HMDB
Ceramide (D18:1,C16:0)	HMDB
Ceramide 16	HMDB
Ceramide(D18:1/16:0)	HMDB
D-Erythro-C16-ceramide	HMDB
D-Erythro-N-hexadecanoylsphingenine	HMDB
D-Erythro-N-palmitoylsphingosine	HMDB
D-Erythro-delta4-ceramide	HMDB
D-Erythro-δ4-ceramide	HMDB
N-Hexadecanoyl-D-erythro-ceramide	HMDB
N-Hexadecanoylsphingosine	HMDB
N-Palmitoyl 4-sphingenine	HMDB
N-Palmitoyl ceramide	HMDB
N-Palmitoyl-D-erythro-sphingosine	HMDB
N-Palmitoyl-D-sphingosine	HMDB
N-(Hexadecanoyl)-sphingosine	MetBuilder
N-(Hexadecanoyl)-D-erythro-sphingosine	MetBuilder
N-(Hexadecanoyl)-4-sphingenine	MetBuilder
N-(Hexadecanoyl)-D-sphingosine	MetBuilder
N-(Hexadecanoyl)-sphingenine	MetBuilder
N-(Hexadecanoyl)-erythro-4-sphingenine	MetBuilder
Cer(D18:1/16:0)	ChEBI

Chemical Formula

C₃₄H₆₇NO₃

Average Molecular Weight

537.9007

Monoisotopic Molecular Weight

537.512095015

IUPAC Name

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

Traditional Name

N-(palmitoyl)-ceramide

CAS Registry Number

4201-58-5

SMILES

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

InChI Identifier

InChI=1S/C34H67NO3/c1-3-5-7-9-11-13-15-17-19-21-23-25-27-29-33(37)32(31-36)35-34(38)30-28-26-24-22-20-18-16-14-12-10-8-6-4-2/h27,29,32-33,36-37H,3-26,28,30-31H2,1-2H3,(H,35,38)/b29-27+/t32-,33+/m0/s1

InChI Key

YDNKGFDKKRUKPY-TURZORIXSA-N

Chemical Taxonomy

Description

belongs to the class of organic compounds known as long-chain ceramides. These are ceramides bearing a long chain fatty acid.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Sphingolipids

Sub Class

Ceramides

Direct Parent

Long-chain ceramides

Alternative Parents

Substituents

Long-chain 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:72959 )
N-acylsphingosines (ceramides) (LMSP02010004 )

Ontology

Status

Detected but not Quantified

Origin

Not Available

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	9.49	ALOGPS
logP	10.87	ChemAxon
logS	-7.1	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	30	ChemAxon
Refractivity	165.78 m³·mol⁻¹	ChemAxon
Polarizability	73.21 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 (2 TMS) - 70eV, Positive	splash10-00y0-4371679000-4350654880fad493e81d	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 20V, Positive	splash10-03di-0090020000-a4c08ce2d2d5bc07212c	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 20V, Positive	splash10-03di-0090020000-6b6cc500a909ad02bd59	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 20V, Positive	splash10-03di-0090020000-4a672523b98af8ff8c7c	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-000i-0000090000-f294f0ced8f149249815	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-01p9-0050090000-80f4b14827e42ec58fea	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-03l0-0090050000-c9f32bf831226119babd	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-000i-0000090000-876883608819d763f04e	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-01p9-0050090000-22ff2434faf08fcef599	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-03l0-0090050000-e6a7f6704ac5e854065c	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-000i-0000090000-15b6716e7356e06043b6	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-000i-0010090000-e14e9c0c2e28b7a12b19	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0ue0-0040090000-a44d6a95bf21d0975da6	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0006-0000090000-d2d11b266d3c5c7e73ff	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0006-0000090000-d2d11b266d3c5c7e73ff	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-004i-0000190000-6ce0a8c6d5140383d837	View in MoNA
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	Not Available	View in JSpectraViewer

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	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	PMID: 31867104	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

HMDB0004949

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB023536

KNApSAcK ID

Not Available

Chemspider ID

4446677

KEGG Compound ID

C00195

BioCyc ID

CERAMIDE

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

PubChem Compound

PDB ID

ChEBI ID

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 (d18:1/16:0) (BMDB0004949)

Structure for BMDB0004949 (Ceramide (d18:1/16:0))

Enzymes