Cannabis Compound Database: Showing Compound Card for CDP-DG(16:0/18:0) (CDB000853)

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Record Information

Version

1.0

Created at

2020-03-30 17:47:12 UTC

Updated at

2020-12-07 19:07:48 UTC

CannabisDB ID

CDB000853

Secondary Accession Numbers

Not Available

Cannabis Compound Identification

Common Name

CDP-DG(16:0/18:0)

Description

CDP-DG(16:0/18:0) belongs to the family of CDP-diacylglycerols. It is a glycerophospholipid containing a diacylglycerol, with a cytidine diphosphate attached to the oxygen O1 or O2 of the glycerol part. As is the case with diacylglycerols, phosphatidylserines can have many different combinations of fatty acids of varying lengths and saturation attached to the C-1 and C-2 positions. CDP-DG(16:0/18:0), in particular, consists of two hexadecanoyl chain at positions C-1 and C2. In E. coli glycerophospholipid metabolism, The biosynthesis of CDP-diacylglycerol (CDP-DG) involves condensation of phosphatidic acid (PA) and cytidine triphosphate, with elimination of pyrophosphate, catalysed by the enzyme CDP-diacylglycerol synthase. The resulting CDP-diacylglycerol can be utilized immediately for the synthesis of phosphatidylglycerol (PG), and thence cardiolipin (CL), and of phosphatidylinositol (PI). CDP-DG(16:0/18:0) is also a substrate of CDP-diacylglycerol pyrophosphatase. It is involved in CDP-diacylglycerol degradation pathway. This compound 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
1-Hexadecanoyl-2-octadecanoyl-sn-glycero-3-CDP	HMDB
1-Palmitoyl-2-stearoyl-sn-glycero-3-cytidine-5'-diphosphate	HMDB
CDP-DG(34:0)	HMDB
CDP-Diacylglycerol(16:0/18:0)	HMDB
CDP-Diacylglycerol(34:0)	HMDB

Chemical Formula

C₄₆H₈₅N₃O₁₅P₂

Average Molecular Weight

982.14

Monoisotopic Molecular Weight

981.5456

IUPAC Name

{[(2R,3R,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}({[(2R)-3-(hexadecanoyloxy)-2-(octadecanoyloxy)propoxy](hydroxy)phosphoryl}oxy)phosphinic acid

Traditional Name

[(2R,3R,5R)-5-(4-amino-2-oxopyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy([(2R)-3-(hexadecanoyloxy)-2-(octadecanoyloxy)propoxy(hydroxy)phosphoryl]oxy)phosphinic acid

CAS Registry Number

Not Available

SMILES

[H][C@@](COC(=O)CCCCCCCCCCCCCCC)(COP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H](C(O)[C@H]1O)N1C=CC(N)=NC1=O)OC(=O)CCCCCCCCCCCCCCCCC

InChI Identifier

InChI=1S/C46H85N3O15P2/c1-3-5-7-9-11-13-15-17-18-20-22-24-26-28-30-32-42(51)62-38(35-59-41(50)31-29-27-25-23-21-19-16-14-12-10-8-6-4-2)36-60-65(55,56)64-66(57,58)61-37-39-43(52)44(53)45(63-39)49-34-33-40(47)48-46(49)54/h33-34,38-39,43-45,52-53H,3-32,35-37H2,1-2H3,(H,55,56)(H,57,58)(H2,47,48,54)/t38-,39-,43+,44?,45-/m1/s1

InChI Key

YRTWPVQQBUGHEO-IOYUWRPMSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as cdp-diacylglycerols. These are glycerolipids containing a diacylglycerol, with a cytidine diphosphate attached to the oxygen O1 or O2 of the glycerol part.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Glycerophospholipids

Sub Class

CDP-glycerols

Direct Parent

CDP-diacylglycerols

Alternative Parents

Substituents

Cdp-diacylglycerol
Pyrimidine ribonucleoside diphosphate
Diacyl-glycerol-3-pyrophosphate
Pentose phosphate
Pentose-5-phosphate
Glycosyl compound
N-glycosyl compound
Monosaccharide phosphate
Organic pyrophosphate
Pentose monosaccharide
Aminopyrimidine
Fatty acid ester
Pyrimidone
Monoalkyl phosphate
Imidolactam
Pyrimidine
Fatty acyl
Alkyl phosphate
Phosphoric acid ester
Dicarboxylic acid or derivatives
Hydropyrimidine
Organic phosphoric acid derivative
Monosaccharide
Tetrahydrofuran
Heteroaromatic compound
Secondary alcohol
Amino acid or derivatives
1,2-diol
Carboxylic acid ester
Organoheterocyclic compound
Azacycle
Oxacycle
Carboxylic acid derivative
Alcohol
Organonitrogen compound
Organic nitrogen compound
Organooxygen compound
Amine
Carbonyl group
Primary amine
Organic oxygen compound
Organopnictogen compound
Hydrocarbon derivative
Organic oxide
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Organoleptic effect:

Touch:

Smooth

Disposition

Route of exposure:

Enteral:

Ingestion

Source:

Biological:

Animal

Biological location:

Biofluid and excreta:

Blood

Tissue and substructures:

All tissues

Cell and elements:

Extracellular

Subcellular:

Role

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
logP	6.43	ALOGPS
logP	10.45	ChemAxon
logS	-5.4	ALOGPS
pKa (Strongest Acidic)	1.86	ChemAxon
pKa (Strongest Basic)	-0.032	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	12	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	263.27 Å²	ChemAxon
Rotatable Bond Count	44	ChemAxon
Refractivity	249.41 m³·mol⁻¹	ChemAxon
Polarizability	109.34 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

EI-MS/GC-MS

Type	Description	Splash Key	View
EI-MS	Mass Spectrum (Electron Ionization)	Not Available	2022-08-06	View Spectrum

MS/MS

Type	Description	Splash Key	View
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-03di-0920000101-dae053f6cfb4b43ac862	2017-09-01	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03di-1920001000-8fa3df355bb346fd2db1	2017-09-01	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-03di-3930000000-bd08cfa0da87b1e46b3d	2017-09-01	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0a5i-0690001103-4dc162520eaf6bcd242b	2017-09-01	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0bti-4692200201-ee0a77da656609148d96	2017-09-01	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0bt9-5921000000-4da85aa01d43da1baba8	2017-09-01	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-01q9-2000010029-e2a2f883320490ad202e	2021-09-22	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-05gi-8010000097-e8ecdaee073af47b6473	2021-09-22	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-00di-0024900000-801b0569c5c4a7c11d3c	2021-09-22	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-001i-0000001009-e6b800c1389bc8a29afe	2021-09-23	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004l-9050611101-9503ba9de5c0152af8bd	2021-09-23	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-015c-8369503102-507cd93bae6867d2fa22	2021-09-23	View Spectrum

NMR

Type	Description	View
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	Spectrum

Pathways

Name	SMPDB/Pathwhiz	KEGG
Cardiolipin Biosynthesis CL(16:0/16:0/16:0/18:0)		Not Available
Cardiolipin Biosynthesis CL(16:0/18:0/16:0/16:1(9Z))		Not Available
Cardiolipin Biosynthesis CL(16:0/18:0/16:0/18:0)		Not Available
Cardiolipin Biosynthesis CL(16:0/18:0/16:0/18:1(11Z))		Not Available
Cardiolipin Biosynthesis CL(16:0/18:0/16:0/18:1(9Z))		Not Available

Protein Targets

Enzymes

Protein Name	Gene Name	Locus	Uniprot ID	Details
Phosphatidate cytidylyltransferase 2	CDS2	20p13	O95674	details
Phosphatidate cytidylyltransferase 1	CDS1	4q21.23	Q92903	details
CDP-diacylglycerol--inositol 3-phosphatidyltransferase	CDIPT	16p11.2	O14735	details
CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase, mitochondrial	PGS1	17q25.3	Q32NB8	details

Transporters

Not Available

Metal Bindings

Not Available

Receptors

Not Available

Transcriptional Factors

Not Available

Concentrations Data

Not Available

External Links

HMDB ID

HMDB0006969

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB024163

KNApSAcK ID

Not Available

Chemspider ID

24765810

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

53477913

PDB ID

Not Available

ChEBI ID

Not Available

References

General References

Not Available

Enzymes

Enzyme Details

1. Phosphatidate cytidylyltransferase 2

General function:: Involved in transferase activity, transferring phosphorus-containing groups
Specific function:: Provides CDP-diacylglycerol an important precursor for the synthesis of phosphatidylinositol, phosphatidylglycerol, and cardiolipin.
Gene Name:: CDS2
Uniprot ID:: O95674
Molecular weight:: 51417.5

Enzyme Details

2. Phosphatidate cytidylyltransferase 1

General function:: Involved in transferase activity, transferring phosphorus-containing groups
Specific function:: Provides CDP-diacylglycerol an important precursor for the synthesis of phosphatidylinositol (PtdIns), phosphatidylglycerol, and cardiolipin. Overexpression may amplify cellular signaling responses from cytokines. May also play an important role in the signal transduction mechanism of retina and neural cells.
Gene Name:: CDS1
Uniprot ID:: Q92903
Molecular weight:: 53303.57

Enzyme Details

3. CDP-diacylglycerol--inositol 3-phosphatidyltransferase

General function:: Involved in phosphotransferase activity, for other substituted phosphate groups
Specific function:: Catalyzes the biosynthesis of phosphatidylinositol (PtdIns) as well as PtdIns:inositol exchange reaction. May thus act to reduce an excessive cellular PtdIns content. The exchange activity is due to the reverse reaction of PtdIns synthase and is dependent on CMP, which is tightly bound to the enzyme.
Gene Name:: CDIPT
Uniprot ID:: O14735
Molecular weight:: 23538.47

Enzyme Details

4. CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase, mitochondrial

General function:: Involved in phosphotransferase activity, for other substituted phosphate groups
Specific function:: Functions in the biosynthesis of the anionic phospholipids phosphatidylglycerol and cardiolipin (By similarity).
Gene Name:: PGS1
Uniprot ID:: Q32NB8
Molecular weight:: 62729.745

Showing Compound Card for CDP-DG(16:0/18:0) (CDB000853)

Structure for CDB000853 (CDP-DG(16:0/18:0))

Enzymes