ChemFOnt: Showing chemical card for CDP-DG(20:3(5Z,8Z,11Z)/20:3(8Z,11Z,14Z)) (CFc000096392)

Record Information

Version

1.0

Creation Date

2022-08-28 10:25:12 UTC

Update Date

2022-09-13 21:09:09 UTC

Chemfont ID

CFc000096392

Molecule Identification

Common Name

CDP-DG(20:3(5Z,8Z,11Z)/20:3(8Z,11Z,14Z))

Definition

CDP-DG(20:3(5Z,8Z,11Z)/20:3(8Z,11Z,14Z)) is a cytidine diphosphate diacylglycerol or CDP-diacylglycerol (CDP-DG). CDP-diacylglycerol is an important branchpoint intermediate in eukaryotic phospholipid biosynthesis and could be a key regulatory molecule in phospholipid metabolism. It is a glycerophospholipid in which a cytidine diphosphate moiety occupies a glycerol substitution site. As is the case with diacylglycerols, CDP-diacylglycerols can have many different combinations of fatty acids of varying lengths and saturation attached at the C-1 and C-2 positions. Fatty acids containing 16, 18 and 20 carbons are the most common. CDP-DG(20:3(5Z,8Z,11Z)/20:3(8Z,11Z,14Z)), in particular, consists of one chain of mead acid at the C-1 position and one chain of dihomo-gamma-linolenic acid at the C-2 position. Cytidine diphosphate diacylglycerols are rarely noticed in analyses of lipid compositions of tissues, as they are present is such small amounts (perhaps only 0.05% or so of the total phospholipids).

Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
1-Meadoyl-2-dihomo-gamma-linolenoyl-sn-glycero-3-CDP	HMDB
1-Meadoyl-2-dihomo-gamma-linolenoyl-sn-glycero-3-cytidine-5'-diphosphate	HMDB
CDP-DG(20:3/20:3)	HMDB
CDP-DG(20:3N9/20:3N6)	HMDB
CDP-DG(20:3W9/20:3W6)	HMDB
CDP-DG(40:6)	HMDB
CDP-Diacylglycerol(20:3(5Z,8Z,11Z)/20:3(8Z,11Z,14Z))	HMDB
CDP-Diacylglycerol(20:3/20:3)	HMDB
CDP-Diacylglycerol(20:3N9/20:3N6)	HMDB
CDP-Diacylglycerol(20:3W9/20:3W6)	HMDB
CDP-Diacylglycerol(40:6)	HMDB
{[(2R,3R,5R)-3,4-dihydroxy-5-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)oxolan-2-yl]methoxy}({hydroxy[(2R)-3-[(5Z,8Z,11Z)-icosa-5,8,11-trienoyloxy]-2-[(8Z,11Z,14Z)-icosa-8,11,14-trienoyloxy]propoxy]phosphoryl}oxy)phosphinate	HMDB
1-meadoyl-2-dihomo-gamma-linolenoyl-sn-glycero-3-CDP	SMPDB, HMDB
1-meadoyl-2-dihomo-gamma-linolenoyl-sn-glycero-3-cytidine-5'-diphosphate	SMPDB, HMDB
CDP-DG(20:3/20:3)	SMPDB, HMDB
CDP-DG(20:3n9/20:3n6)	SMPDB, HMDB
CDP-DG(20:3w9/20:3w6)	SMPDB, HMDB
CDP-DG(40:6)	SMPDB, HMDB
CDP-diacylglycerol(20:3(5Z,8Z,11Z)/20:3(8Z,11Z,14Z))	SMPDB, HMDB
CDP-diacylglycerol(20:3/20:3)	SMPDB, HMDB
CDP-diacylglycerol(20:3n9/20:3n6)	SMPDB, HMDB
CDP-diacylglycerol(20:3w9/20:3w6)	SMPDB, HMDB
CDP-DG(20:3(5Z,8Z,11Z)/20:3(8Z,11Z,14Z))	SMPDB

Chemical Formula

C₅₂H₈₅N₃O₁₅P₂

Average Molecular Weight

1054.206

Monoisotopic Molecular Weight

1053.545593045

IUPAC Name

{[(2R,3R,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}({hydroxy[(2R)-3-[(5Z,8Z,11Z)-icosa-5,8,11-trienoyloxy]-2-[(8Z,11Z,14Z)-icosa-8,11,14-trienoyloxy]propoxy]phosphoryl}oxy)phosphinic acid

Traditional Name

[(2R,3R,5R)-5-(4-amino-2-oxopyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy([hydroxy((2R)-3-[(5Z,8Z,11Z)-icosa-5,8,11-trienoyloxy]-2-[(8Z,11Z,14Z)-icosa-8,11,14-trienoyloxy]propoxy)phosphoryl]oxy)phosphinic acid

CAS Registry Number

Not Available

SMILES

[H][C@@](COC(=O)CCC\C=C/C\C=C/C\C=C/CCCCCCCC)(COP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H](C(O)[C@H]1O)N1C=CC(N)=NC1=O)OC(=O)CCCCCC\C=C/C\C=C/C\C=C/CCCCC

InChI Identifier

InChI=1S/C52H85N3O15P2/c1-3-5-7-9-11-13-15-17-19-21-23-25-27-29-31-33-35-37-47(56)65-41-44(68-48(57)38-36-34-32-30-28-26-24-22-20-18-16-14-12-10-8-6-4-2)42-66-71(61,62)70-72(63,64)67-43-45-49(58)50(59)51(69-45)55-40-39-46(53)54-52(55)60/h12,14,17-20,23-26,29,31,39-40,44-45,49-51,58-59H,3-11,13,15-16,21-22,27-28,30,32-38,41-43H2,1-2H3,(H,61,62)(H,63,64)(H2,53,54,60)/b14-12-,19-17-,20-18-,25-23-,26-24-,31-29-/t44-,45-,49+,50?,51-/m1/s1

InChI Key

IIKCFUPQVLBEBQ-VZDUTLNTSA-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

Functional Ontology

Not Available

Endogenous (HMDB: HMDB0115983)

Process

Naturally occurring process

Not Available

Physical Properties

Predicted Properties

Property	Value	Source
Water Solubility	0.0012 g/L	ALOGPS
logP	7.33	ALOGPS
logP	10.94	ChemAxon
logS	-6	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	283.72 m³·mol⁻¹	ChemAxon
Polarizability	114.3 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

External Links

HMDB ID

HMDB0115983

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

74877721

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

131822639

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

Showing chemical card for CDP-DG(20:3(5Z,8Z,11Z)/20:3(8Z,11Z,14Z)) (CFc000096392)

MOL for CFc000096392 (CDP-DG(20:3(5Z,8Z,11Z)/20:3(8Z,11Z,14Z)))

3D MOL for CFc000096392 (CDP-DG(20:3(5Z,8Z,11Z)/20:3(8Z,11Z,14Z)))

3D SDF for CFc000096392 (CDP-DG(20:3(5Z,8Z,11Z)/20:3(8Z,11Z,14Z)))

3D-SDF for CFc000096392 (CDP-DG(20:3(5Z,8Z,11Z)/20:3(8Z,11Z,14Z)))

PDB for CFc000096392 (CDP-DG(20:3(5Z,8Z,11Z)/20:3(8Z,11Z,14Z)))

3D PDB for CFc000096392 (CDP-DG(20:3(5Z,8Z,11Z)/20:3(8Z,11Z,14Z)))

SMILES for CFc000096392 (CDP-DG(20:3(5Z,8Z,11Z)/20:3(8Z,11Z,14Z)))

INCHI for CFc000096392 (CDP-DG(20:3(5Z,8Z,11Z)/20:3(8Z,11Z,14Z)))

Structure for CFc000096392 (CDP-DG(20:3(5Z,8Z,11Z)/20:3(8Z,11Z,14Z)))

3D Structure for CFc000096392 (CDP-DG(20:3(5Z,8Z,11Z)/20:3(8Z,11Z,14Z)))