Cannabis Compound Database: Showing Compound Card for 3-Dehydrosphinganine (CDB004917)

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Record Information

Version

1.0

Created at

2020-04-17 18:50:16 UTC

Updated at

2020-12-07 19:11:16 UTC

CannabisDB ID

CDB004917

Secondary Accession Numbers

Not Available

Cannabis Compound Identification

Common Name

3-Dehydrosphinganine

Description

3-Dehydrosphinganine, also known as KDHS or ketodihydrosphingosine, belongs to the class of organic compounds known as beta-hydroxy ketones. These are ketones containing a hydroxyl group attached to the beta-carbon atom, relative to the C=O group. Thus, 3-dehydrosphinganine is considered to be a sphingoid base lipid molecule. 3-Dehydrosphinganine is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral. 3-Dehydrosphinganine exists in all eukaryotes, ranging from yeast to humans. Within humans, 3-dehydrosphinganine participates in a number of enzymatic reactions. In particular, 3-dehydrosphinganine and carbon dioxide can be biosynthesized from palmityl-CoA and L-serine through the action of the enzyme serine palmitoyltransferase 1. In addition, 3-dehydrosphinganine can be biosynthesized from sphinganine; which is catalyzed by the enzyme 3-ketodihydrosphingosine reductase. In humans, 3-dehydrosphinganine is involved in the metabolic disorder called the krabbe disease pathway. Outside of the human body, 3-Dehydrosphinganine has been detected, but not quantified in, several different foods, such as common chokecherries, black huckleberries, pomegranates, cinnamons, and flaxseeds. This could make 3-dehydrosphinganine a potential biomarker for the consumption of these foods. A 2-amino-1-hydroxyoctadecan-3-one that has S-configuration. 3-Dehydrosphinganine is expected to be in Cannabis as all living plants are known to produce and metabolize it.

Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
3-Dehydro-D-sphinganine	ChEBI
3-Ketodihydrosphingosine	ChEBI
3-Ketosphinganine	ChEBI
(2S)-2-Amino-1-hydroxyoctadecan-3-one	HMDB
1-Hydroxy-2-amino-3-oxo-octadecane	HMDB
2-Amino-1-hydroxy-3-octadecanone	HMDB
KDHS	HMDB
Ketodihydrosphingosine	HMDB
(+-)-Isomer OF ketodihydrosphingosine	HMDB
(S)-Isomer OF ketodihydrosphingosine	HMDB

Chemical Formula

C₁₈H₃₇NO₂

Average Molecular Weight

299.49

Monoisotopic Molecular Weight

299.2824

IUPAC Name

(2S)-2-amino-1-hydroxyoctadecan-3-one

Traditional Name

3-ketosphinganine

CAS Registry Number

16105-69-4

SMILES

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

InChI Identifier

InChI=1S/C18H37NO2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-18(21)17(19)16-20/h17,20H,2-16,19H2,1H3/t17-/m0/s1

InChI Key

KBUNOSOGGAARKZ-KRWDZBQOSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as beta-hydroxy ketones. These are ketones containing a hydroxyl group attached to the beta-carbon atom, relative to the C=O group.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbonyl compounds

Direct Parent

Beta-hydroxy ketones

Alternative Parents

Substituents

Beta-hydroxy ketone
Alpha-aminoketone
Organic nitrogen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Primary amine
Primary alcohol
Organonitrogen compound
Primary aliphatic amine
Amine
Alcohol
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

2-amino-1-hydroxyoctadecan-3-one (CHEBI:17862 )
Sphing-4-enines (Sphingosines) (C02934 )
Sphinganines (LMSP01020002 )

Ontology

Disposition

Route of exposure:

Enteral:

Ingestion

Source:

Biological:

Animal

Extracellular

Role

Industrial application:

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
logP	5.45	ALOGPS
logP	5.18	ChemAxon
logS	-5.4	ALOGPS
pKa (Strongest Acidic)	14.38	ChemAxon
pKa (Strongest Basic)	7.54	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	63.32 Å²	ChemAxon
Rotatable Bond Count	16	ChemAxon
Refractivity	90.03 m³·mol⁻¹	ChemAxon
Polarizability	39.56 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

EI-MS/GC-MS

Type	Description	Splash Key	View
Predicted GC-MS	3-Dehydrosphinganine, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positive	splash10-01p9-9120000000-135052b999433b5dd30b	Spectrum
Predicted GC-MS	3-Dehydrosphinganine, 1 TMS, Predicted GC-MS Spectrum - 70eV, Positive	splash10-03di-9321000000-e0d96cb3bea3c320412a	Spectrum
Predicted GC-MS	3-Dehydrosphinganine, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	3-Dehydrosphinganine, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum

MS/MS

Type	Description	Splash Key	View
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0f89-2096000000-8323a157b44b31f2331a	2016-09-12	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-01qa-4491000000-39be7a6025f78d062cb5	2016-09-12	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-01ox-9510000000-a675e52903f069501f67	2016-09-12	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0002-1090000000-e36f44a44812cc09023c	2016-09-12	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-015j-4090000000-4a24200105a7fd0afd1e	2016-09-12	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-052f-9020000000-edd2ec1e7a7fae113d2f	2016-09-12	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0ue9-3069000000-e43a689cbba7742dc5c6	2021-09-22	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-01q9-9282000000-f83e19a33602a8a25cb8	2021-09-22	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a4l-9000000000-f16a410d8c3330af51f2	2021-09-22	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-014j-0090000000-7d1c46d2460baf58b0dc	2021-09-22	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-06ej-3090000000-b775508a0489f38a77f7	2021-09-22	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0a4l-9010000000-b10c9eb2adca17092c8c	2021-09-22	View Spectrum

NMR

Not Available

Pathways

Name	SMPDB/Pathwhiz	KEGG
Sphingolipid Metabolism
Gaucher Disease		Not Available
Globoid Cell Leukodystrophy		Not Available
Metachromatic Leukodystrophy (MLD)		Not Available
Fabry disease		Not Available

Protein Targets

Enzymes

Protein Name	Gene Name	Locus	Uniprot ID	Details
Globoside alpha-1,3-N-acetylgalactosaminyltransferase 1	GBGT1	9q34.13-q34.3	Q8N5D6	details
N-acetylglucosaminyl-phosphatidylinositol de-N-acetylase	PIGL	17p12-p11.2	Q9Y2B2	details
Serine palmitoyltransferase 1	SPTLC1	9q22.2	O15269	details
Serine palmitoyltransferase 2	SPTLC2	14q24.3	O15270	details
Phosphatidylinositol N-acetylglucosaminyltransferase subunit Q	PIGQ	16p13.3	Q9BRB3	details
Phosphatidylinositol N-acetylglucosaminyltransferase subunit A	PIGA	Xp22.1	P37287	details
Phosphatidylinositol N-acetylglucosaminyltransferase subunit H	PIGH	14q24.1	Q14442	details
Phosphatidylinositol N-acetylglucosaminyltransferase subunit P	PIGP	21q22.2	P57054	details
Phosphatidylinositol N-acetylglucosaminyltransferase subunit C	PIGC	1q23-q25	Q92535	details
Ganglioside GM2 activator	GM2A	5q33.1	P17900	details
T-cell surface glycoprotein CD1e, membrane-associated	CD1E	1q22-q23	P15812	details
Epididymal secretory protein E1	NPC2	14q24.3	P61916	details
Antigen-presenting glycoprotein CD1d	CD1D	1q22-q23	P15813	details
GPI mannosyltransferase 1	PIGM	1q23.2	Q9H3S5	details
Phosphatidylinositol-glycan biosynthesis class W protein	PIGW		Q7Z7B1	details
3-ketodihydrosphingosine reductase	KDSR	18q21.3	Q06136	details
Phosphatidylinositol-glycan biosynthesis class X protein	PIGX	3q29	Q8TBF5	details
GPI mannosyltransferase 4	PIGZ	3q29	Q86VD9	details
Lactosylceramide 1,3-N-acetyl-beta-D-glucosaminyltransferase	B3GNT5	3q28	Q9BYG0	details
Beta-1,3-galactosyltransferase 5	B3GALT5	21q22.3	Q9Y2C3	details
GPI mannosyltransferase 3	PIGB	15q21-q22	Q92521	details
Phosphatidylinositol-glycan biosynthesis class F protein	PIGF	2p21-p16	Q07326	details
GPI ethanolamine phosphate transferase 2	PIGG	4p16.3	Q5H8A4	details
GPI ethanolamine phosphate transferase 1	PIGN	18q21.33	O95427	details
GPI ethanolamine phosphate transferase 3	PIGO	9p13.3	Q8TEQ8	details
GPI transamidase component PIG-S	PIGS	17p13.2	Q96S52	details
GPI transamidase component PIG-T	PIGT	20q12-q13.12	Q969N2	details
Phosphatidylinositol glycan anchor biosynthesis class U protein	PIGU	20q11.22	Q9H490	details
GPI mannosyltransferase 2	PIGV	1p36.11	Q9NUD9	details
Phosphatidylinositol N-acetylglucosaminyltransferase subunit Y	PIGY	4q22.1	Q3MUY2	details
Serine palmitoyltransferase 3	SPTLC3	20p12.1	Q9NUV7	details
Non-lysosomal glucosylceramidase	GBA2	9p13.3	Q9HCG7	details
GPI-anchor transamidase	PIGK	1p31.1	Q92643	details

Transporters

Protein Name	Gene Name	Locus	Uniprot ID	Details
Pleckstrin homology domain-containing family A member 8	PLEKHA8	7p21-p11.2	Q96JA3	details
Protein PLEKHA9	PLEKHA9	12q	O95397	details
Glycolipid transfer protein domain-containing protein 2	GLTPD2	17p13.2	A6NH11	details
Putative uncharacterized protein PLEKHA8	PLEKHA8	7p21-p11.2	B5MDU3	details
Glycolipid transfer protein domain-containing protein 1	GLTPD1	1p36.33	Q5TA50	details
Putative uncharacterized protein DKFZp434L0435	DKFZp434L0435		Q9UFH6	details
Glycolipid transfer protein	GLTP	12q24.11	Q9NZD2	details

Metal Bindings

Not Available

Receptors

Not Available

Transcriptional Factors

Not Available

Concentrations Data

Not Available

External Links

HMDB ID

HMDB0001480

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB022645

KNApSAcK ID

Not Available

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Wikipedia Link

Not Available

METLIN ID

3428

PubChem Compound

439853

PDB ID

Not Available

ChEBI ID

17862

References

General References

Not Available

Only showing the first 10 proteins. There are 40 proteins in total.

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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. Serine palmitoyltransferase 1

General function:: Involved in transferase activity, transferring nitrogenous groups
Specific function:: Serine palmitoyltransferase (SPT). The heterodimer formed with SPTLC2 or SPTLC3 constitutes the catalytic core. The composition of the serine palmitoyltransferase (SPT) complex determines the substrate preference. The SPTLC1-SPTLC2-SPTSSA complex shows a strong preference for C16-CoA substrate, while the SPTLC1-SPTLC3-SPTSSA isozyme uses both C14-CoA and C16-CoA as substrates, with a slight preference for C14-CoA. The SPTLC1-SPTLC2-SPTSSB complex shows a strong preference for C18-CoA substrate, while the SPTLC1-SPTLC3-SPTSSB isozyme displays an ability to use a broader range of acyl-CoAs, without apparent preference.
Gene Name:: SPTLC1
Uniprot ID:: O15269
Molecular weight:: 52743.41

Enzyme Details

4. Serine palmitoyltransferase 2

General function:: Involved in transferase activity
Specific function:: Serine palmitoyltransferase (SPT). The heterodimer formed with LCB1/SPTLC1 constitutes the catalytic core. The composition of the serine palmitoyltransferase (SPT) complex determines the substrate preference. The SPTLC1-SPTLC2-SPTSSA complex shows a strong preference for C16-CoA substrate, while the SPTLC1-SPTLC2-SPTSSB complex displays a preference for C18-CoA substrate.
Gene Name:: SPTLC2
Uniprot ID:: O15270
Molecular weight:: 62923.765

Enzyme Details

5. 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

6. 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

7. 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

8. 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

Enzyme Details

9. Phosphatidylinositol N-acetylglucosaminyltransferase subunit C

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

Enzyme Details

10. Ganglioside GM2 activator

General function:: Involved in sphingolipid activator protein activity
Specific function:: Binds gangliosides and stimulates ganglioside GM2 degradation. It stimulates only the breakdown of ganglioside GM2 and glycolipid GA2 by beta-hexosaminidase A. It extracts single GM2 molecules from membranes and presents them in soluble form to beta-hexosaminidase A for cleavage of N-acetyl-D-galactosamine and conversion to GM3
Gene Name:: GM2A
Uniprot ID:: P17900
Molecular weight:: 20838.1

Transporters

Enzyme Details

1. Pleckstrin homology domain-containing family A member 8

General function:: Involved in glycolipid transporter activity
Specific function:: Involved in TGN-to-plasma membrane transport and in the formation of post-Golgi constitutive carriers. May play a role in ensuring the coordination of the budding and the fission reactions
Gene Name:: PLEKHA8
Uniprot ID:: Q96JA3
Molecular weight:: 58306.0

Enzyme Details

2. Protein PLEKHA9

General function:: Involved in glycolipid transporter activity
Specific function:: Not Available
Gene Name:: PLEKHA9
Uniprot ID:: O95397
Molecular weight:: 43538.3

Enzyme Details

3. Glycolipid transfer protein domain-containing protein 2

General function:: Involved in glycolipid transporter activity
Specific function:: Not Available
Gene Name:: GLTPD2
Uniprot ID:: A6NH11
Molecular weight:: 31641.2

Enzyme Details

4. Putative uncharacterized protein PLEKHA8

General function:: Involved in glycolipid transporter activity
Specific function:: Not Available
Gene Name:: PLEKHA8
Uniprot ID:: B5MDU3
Molecular weight:: 49308.8

Enzyme Details

5. Glycolipid transfer protein domain-containing protein 1

General function:: Involved in glycolipid transporter activity
Specific function:: Not Available
Gene Name:: GLTPD1
Uniprot ID:: Q5TA50
Molecular weight:: 24364.8

Enzyme Details

6. Putative uncharacterized protein DKFZp434L0435

General function:: Involved in glycolipid transporter activity
Specific function:: Not Available
Gene Name:: DKFZp434L0435
Uniprot ID:: Q9UFH6
Molecular weight:: 6175.1

Enzyme Details

7. Glycolipid transfer protein

General function:: Involved in glycolipid transporter activity
Specific function:: Accelerates the intermembrane transfer of various glycolipids. Catalyzes the transfer of various glycosphingolipids between membranes but does not catalyze the transfer of phospholipids. May be involved in the intracellular translocation of glucosylceramides
Gene Name:: GLTP
Uniprot ID:: Q9NZD2
Molecular weight:: 23849.6

Only showing the first 10 proteins. There are 40 proteins in total.

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Showing Compound Card for 3-Dehydrosphinganine (CDB004917)

Structure for CDB004917 (3-Dehydrosphinganine)

Enzymes

Transporters