P. aeruginosa Metabolome Database: CDP-DG(19:1(9Z)/16:0) (PAMDB003777)

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

PAMDB003777

Identification

Name:

CDP-DG(19:1(9Z)/16:0)

Description:

CDP-DG(19:1(9Z)/16:0) 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 atoms. CDP-DG(19:1(9Z)/16:0), in particular, consists of one 9Z-nonadecenoyl chain to C-1 atom, and one hexadecanoyl 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(19:1(9Z)/16:0) 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:

1-(9Z-nonadecenoyl)-2-hexadecanoyl-sn-glycero-3-CDP
1-(9Z-nonadecenoyl)-2-hexadecanoyl-sn-glycero-3-cytidine-5'-diphosphate
1-(9Z-Nonadecenoyl)-2-hexadecanoyl-sn-glycero-3-cytidine-5'-diphosphoric acid
1-9Z-nonadecenoyl-2-palmitoyl-sn-glycero-3-cytidine-5'-diphosphate
1-9Z-Nonadecenoyl-2-palmitoyl-sn-glycero-3-cytidine-5'-diphosphoric acid
CDP-DG(19:1/16:0)
CDP-DG(35:1)
CDP-Diacylglycerol(19:1/16:0)
CDP-Diacylglycerol(35:1)

Chemical Formula:

C₄₇H₈₅N₃O₁₅P₂

Average Molecular Weight:

994.151

Monoisotopic Molecular Weight:

993.545593045

InChI Key:

JVAWHZXYSFYEKE-CPRFLNEQSA-N

InChI:

InChI=1S/C47H85N3O15P2/c1-3-5-7-9-11-13-15-17-18-19-21-22-24-26-28-30-32-42(51)60-36-39(63-43(52)33-31-29-27-25-23-20-16-14-12-10-8-6-4-2)37-61-66(56,57)65-67(58,59)62-38-40-44(53)45(54)46(64-40)50-35-34-41(48)49-47(50)55/h18-19,34-35,39-40,44-46,53-54H,3-17,20-33,36-38H2,1-2H3,(H,56,57)(H,58,59)(H2,48,49,55)/b19-18-/t39-,40-,44+,45?,46-/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)-2-(hexadecanoyloxy)-3-[(9Z)-nonadec-9-enoyloxy]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)-2-(hexadecanoyloxy)-3-[(9Z)-nonadec-9-enoyloxy]propoxy(hydroxy)phosphoryl]oxy)phosphinic acid

SMILES:

[H][C@@](COC(=O)CCCCCCC\C=C/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)CCCCCCCCCCCCCCC

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
Organic pyrophosphate
Monosaccharide phosphate
Fatty acid ester
Hydroxypyrimidine
Monoalkyl phosphate
Alkyl phosphate
Organic phosphoric acid derivative
Monosaccharide
Pyrimidine
Phosphoric acid ester
Fatty acyl
Hydropyrimidine
Dicarboxylic acid or derivatives
Heteroaromatic compound
Oxolane
Secondary alcohol
1,2-diol
Carboxylic acid ester
Organoheterocyclic compound
Azacycle
Oxacycle
Carboxylic acid derivative
Alcohol
Hydrocarbon derivative
Organic oxide
Organic oxygen compound
Organic nitrogen compound
Carbonyl group
Organonitrogen compound
Organooxygen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

Physical Properties

State:

Solid

Charge:

-2

Melting point:

Not Available

Experimental Properties:

Property	Value	Source

Predicted Properties

Property	Value	Source
Water Solubility	0.00358 mg/mL	ALOGPS
logP	6.7	ALOGPS
logP	10.53	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	255.13 m³·mol^-1	ChemAxon
Polarizability	109.27 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:

DG(19:1(9Z)/16:0/0:0) + Cytidine triphosphate + Hydrogen ion > CDP-DG(19:1(9Z)/16:0) + Pyrophosphate

Pathways:

Glycerophospholipid metabolism pae00564

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
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

Enzymes

Protein Details

• Phosphatidate cytidylyltransferase

General function:: Involved in transferase activity, transferring phosphorus-containing groups
Specific function:: CTP + phosphatidate = diphosphate + CDP- diacylglycerol
Gene Name:: cdsA
Locus Tag:: PA3651
Molecular weight:: 28.9 kDa

Reactions

CTP + phosphatidate = diphosphate + CDP-diacylglycerol.

Protein Details

• CDP-diacylglycerol--serine O-phosphatidyltransferase

General function:: Involved in phosphotransferase activity, for other substituted phosphate groups
Specific function:: CDP-diacylglycerol + L-serine = CMP + (3-sn- phosphatidyl)-L-serine
Gene Name:: pssA
Locus Tag:: PA4693
Molecular weight:: 29.3 kDa

Reactions

CDP-diacylglycerol + L-serine = CMP + (3-sn-phosphatidyl)-L-serine.

Transporters

Protein Details

• Probable phospholipid ABC transporter permease protein mlaE

General function:: Secondary metabolites biosynthesis, transport and catabolism
Specific function:: Part of the ABC transporter complex mlaFEDB that actively prevents phospholipid accumulation at the cell surface. Probably maintains lipid asymmetry in the outer membrane by retrograde trafficking of phospholipids from the outer membrane to the inner membrane
Gene Name:: mlaE
Locus Tag:: PA4455
Molecular weight:: 28.4 kDa

CDP-DG(19:1(9Z)/16:0) (PAMDB003777)

Structure for CDP-DG(19:1(9Z)/16:0) (PAMDB003777)

Enzymes

Reactions

Reactions

Transporters