P. aeruginosa Metabolome Database: CDP-DG(10:0/10:0(3-OH)) (PAMDB006756)

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

PAMDB006756

Identification

Name:

CDP-DG(10:0/10:0(3-OH))

Description:

CDP-DG(10:0/10:0(3-OH)) 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 atoms. CDP-DG(10:0/10:0(3-OH)), in particular, consists of one decanoyl chain to C-1 atom, and one 3-hydroxydecanoyl to the C-2 atom. In Pseudomonas aeruginosa 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(10:0/10:0(3-OH)) is also a substrate of CDP-diacylglycerol pyrophosphatase. It is involved in CDP-diacylglycerol degradation pathway.

Structure

🔍MOL SDF PDB SMILES InChI View Structure

Synonyms:

Not Available

Chemical Formula:

C₃₂H₅₇N₃O₁₆P₂

Average Molecular Weight:

801.761

Monoisotopic Molecular Weight:

801.321406763

InChI Key:

QCIVGUHYBOTVSE-WCNNHDROSA-N

InChI:

InChI=1S/C32H57N3O16P2/c1-3-5-7-9-10-12-14-16-27(37)46-20-24(49-28(38)19-23(36)15-13-11-8-6-4-2)21-47-52(42,43)51-53(44,45)48-22-25-29(39)30(40)31(50-25)35-18-17-26(33)34-32(35)41/h17-18,23-25,29-31,36,39-40H,3-16,19-22H2,1-2H3,(H,42,43)(H,44,45)(H2,33,34,41)/t23?,24-,25-,29+,30?,31-/m1/s1

CAS number:

Not Available

IUPAC Name:

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

Traditional IUPAC Name:

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

SMILES:

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

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
Diacyl-glycerol-3-pyrophosphate
Pentose phosphate
Pentose-5-phosphate
Glycosyl compound
N-glycosyl compound
Monosaccharide phosphate
Organic pyrophosphate
Beta-hydroxy acid
Fatty acid ester
Hydroxypyrimidine
Monoalkyl phosphate
Fatty acyl
Alkyl phosphate
Pyrimidine
Phosphoric acid ester
Dicarboxylic acid or derivatives
Hydropyrimidine
Hydroxy acid
Monosaccharide
Organic phosphoric acid derivative
Heteroaromatic compound
Oxolane
Secondary alcohol
1,2-diol
Carboxylic acid ester
Oxacycle
Organoheterocyclic compound
Carboxylic acid derivative
Azacycle
Organooxygen compound
Organic oxide
Organic oxygen compound
Alcohol
Organic nitrogen compound
Carbonyl group
Organonitrogen compound
Hydrocarbon derivative
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	0.73 mg/mL	ALOGPS
logP	1.89	ALOGPS
logP	2.99	ChemAxon
logS	-3	ALOGPS
pKa (Strongest Acidic)	-0.032	ChemAxon
pKa (Strongest Basic)	3.27	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	13	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	283.5 Å²	ChemAxon
Rotatable Bond Count	30	ChemAxon
Refractivity	186.51 m³·mol^-1	ChemAxon
Polarizability	81.3 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:

Cytoplasm

Reactions:

2 DG(10:0/10:0(3-OH)/0:0) + Cytidine triphosphate + Hydrogen ion >2 CDP-DG(10:0/10:0(3-OH)) + Pyrophosphate
2 CDP-DG(10:0/10:0(3-OH)) + Glycerol 3-phosphate >2 PGP(10:0/10:0(3-OH)) + Cytidine monophosphate + Hydrogen ion + Cytidine monophosphate

Pathways:

Not Available

Spectra

Spectra:

References

References:

Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. Pubmed: 22080510
Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590. Pubmed: 21097882
Uniprot Consortium (2012). "Reorganizing the protein space at the Universal Protein Resource (UniProt)." Nucleic Acids Res 40:D71-D75. Pubmed: 22102590
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-DG(10:0/10:0(3-OH)) (PAMDB006756)

Structure for CDP-DG(10:0/10:0(3-OH)) (PAMDB006756)