P. aeruginosa Metabolome Database: CDP-1,2-didodecanoylglycerol (PAMDB001596)

Identification Taxonomy Physical Properties Biological Properties Spectra Concentrations Links References Enzymes Transporters

Proteins (3280)

Record Information

Version

1.0

Update Date

1/22/2018 11:54:54 AM

Metabolite ID

PAMDB001596

Identification

Name:

CDP-1,2-didodecanoylglycerol

Description:

Cdp-1,2-didodecanoylglycerol belongs to the class of CDP-Diacylglycerols. These are glycerolipids containing a diacylglycerol, with a cytidine diphosphate attached to the oxygen O1 or O2 of the glycerol part. (inferred from compound structure)

Structure

🔍MOL SDF PDB SMILES InChI View Structure

Synonyms:

Not Available

Chemical Formula:

C₃₆H₆₅N₃O₁₅P₂

Average Molecular Weight:

841.8599

Monoisotopic Molecular Weight:

841.389091449

InChI Key:

PTPPKXVNJJIECF-LSSKPTOFSA-N

InChI:

InChI=1S/C36H65N3O15P2/c1-3-5-7-9-11-13-15-17-19-21-31(40)49-25-28(52-32(41)22-20-18-16-14-12-10-8-6-4-2)26-50-55(45,46)54-56(47,48)51-27-29-33(42)34(43)35(53-29)39-24-23-30(37)38-36(39)44/h23-24,28-29,33-35,42-43H,3-22,25-27H2,1-2H3,(H,45,46)(H,47,48)(H2,37,38,44)/t28-,29-,33-,34-,35-/m1/s1

CAS number:

Not Available

IUPAC Name:

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

Traditional IUPAC Name:

{[(2R,3S,4R,5R)-5-(4-amino-2-oxopyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy(2R)-2,3-bis(dodecanoyloxy)propoxyphosphinic acid

SMILES:

CCCCCCCCCCCC(=O)OC[C@H](COP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C=CC(N)=NC1=O)OC(=O)CCCCCCCCCCC

Chemical Taxonomy

Taxonomy Description

This compound 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
N-glycosyl compound
Glycosyl compound
Organic pyrophosphate
Monosaccharide phosphate
Monoalkyl phosphate
Pyrimidone
Fatty acid ester
Aminopyrimidine
Fatty acyl
Imidolactam
Alkyl phosphate
Pyrimidine
Primary aromatic amine
Phosphoric acid ester
Organic phosphoric acid derivative
Organic phosphate
Monosaccharide
Hydropyrimidine
Dicarboxylic acid or derivatives
Saccharide
Heteroaromatic compound
Oxolane
Secondary alcohol
Carboxylic acid ester
1,2-diol
Oxacycle
Azacycle
Organoheterocyclic compound
Carboxylic acid derivative
Hydrocarbon derivative
Primary amine
Organooxygen compound
Organonitrogen compound
Carbonyl group
Amine
Alcohol
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

Physical Properties

State:

Not Available

Charge:

-2

Melting point:

Not Available

Experimental Properties:

Property	Value	Source

Predicted Properties

Property	Value	Source
Water Solubility	0.0853 mg/mL	ALOGPS
logP	3.78	ALOGPS
logP	5.73	ChemAxon
logS	-4	ALOGPS
pKa (Strongest Acidic)	1.86	ChemAxon
pKa (Strongest Basic)	-0.52	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	34	ChemAxon
Refractivity	203.4 m³·mol^-1	ChemAxon
Polarizability	86.93 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	0	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Biological Properties

Cellular Locations:

Membrane

Reactions:

Cytidine triphosphate + Hydrogen ion + PA(16:0/16:0) > CDP-1,2-didodecanoylglycerol + Pyrophosphate
CDP-1,2-didodecanoylglycerol + Glycerol 3-phosphate > Cytidine monophosphate + Hydrogen ion + PGP(12:0/12:0)
CDP-1,2-didodecanoylglycerol + L-Serine > Cytidine monophosphate + Hydrogen ion + PS(16:0/16:0)
CDP-1,2-didodecanoylglycerol + Water > Cytidine monophosphate +2 Hydrogen ion + PA(16:0/16:0)
2 DG(12:0/12:0/0:0) + Cytidine triphosphate + Hydrogen ion >2 CDP-1,2-didodecanoylglycerol + Pyrophosphate
2 CDP-1,2-didodecanoylglycerol + Glycerol 3-phosphate >2 PGP(12:0/12:0) + Cytidine monophosphate + Hydrogen ion + Cytidine monophosphate

Pathways:

Not Available

Spectra

Spectra:

Spectrum Type	Description	Splash Key
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-03di-0900001010-903f4758ee3c8f4e97a3	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03di-1900000000-e13f2ee21e9108abb203	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-03di-2920000000-fc72c3890c6df31f223d	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0bu4-0900002110-7e32c57b209b0ce7bbbb	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-01ot-2901110000-af3d7258a954a21ffcdf	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0bvi-4900000000-23afda044a3033394634	View in MoNA

References

References:

Yurtsever D. (2007). Fatty acid methyl ester profiling of Enterococcus and Esherichia coli for microbial source tracking. M.sc. Thesis. Villanova University: U.S.A

Synthesis Reference:

Not Available

Material Safety Data Sheet (MSDS)

Not Available

Links

External Links:

Resource	Link
CHEBI ID	Not Available
HMDB ID	Not Available
Pubchem Compound ID	Not Available
Kegg ID	Not Available
ChemSpider ID	Not Available
Wikipedia ID	Not Available
BioCyc ID	Not Available

CDP-1,2-didodecanoylglycerol (PAMDB001596)

Structure for CDP-1,2-didodecanoylglycerol (PAMDB001596)