ECMDB: CDP-DG(18:1(11Z)/22:6(4Z,7Z,10Z,13Z,16Z,19Z)) (ECMDB06994) (M2MDB000734)

Identification Taxonomy Physical Properties Biological Properties Spectra Concentrations Links References Enzymes (4)Transporters (3)XML

Proteins (7)

Record Information

Version

2.0

Creation Date

2012-05-31 14:12:00 -0600

Update Date

2015-09-18 13:41:01 -0600

Secondary Accession Numbers

ECMDB06994

Identification

Name:

CDP-DG(18:1(11Z)/22:6(4Z,7Z,10Z,13Z,16Z,19Z))

Description

CDP-DG(18:1(11Z)/22:6(4Z,7Z,10Z,13Z,16Z,19Z)) 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(18:1(11Z)/22:6(4Z,7Z,10Z,13Z,16Z,19Z)), in particular, consists of one 11Z-octadecenoyl chain to C-1 atom, and one 4Z,7Z,10Z,13Z,16Z,19Z-docosahexaenoyl to the C-2 atom. 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(18:1(11Z)/22:6(4Z,7Z,10Z,13Z,16Z,19Z)) is also a substrate of CDP-diacylglycerol pyrophosphatase. It is involved in CDP-diacylglycerol degradation pathway.

Structure

MOL SDF PDB SMILES InChI

Synonyms:

1-(11Z-Octadecenoyl)-2-(4Z,7Z,10Z,13Z,16Z,19Z-docosahexaenoyl)-sn-glycero-3-CDP
1-(11Z-octadecenoyl)-2-(4Z,7Z,10Z,13Z,16Z,19Z-docosahexaenoyl)-sn-glycero-3-cytidine-5'-diphosphate
1-(11Z-Octadecenoyl)-2-(4Z,7Z,10Z,13Z,16Z,19Z-docosahexaenoyl)-sn-glycero-3-cytidine-5'-diphosphoric acid
1-Vaccenoyl-2-docosahexaenoyl-sn-glycero-3-cytidine-5'-diphosphate
1-Vaccenoyl-2-docosahexaenoyl-sn-glycero-3-cytidine-5'-diphosphoric acid
CDP-DG(18:1/22:6)
CDP-DG(18:1n7/22:6n3)
CDP-DG(18:1w7/22:6w3)
CDP-DG(40:7)
CDP-Diacylglycerol(18:1/22:6)
CDP-Diacylglycerol(18:1n7/22:6n3)
CDP-Diacylglycerol(18:1w7/22:6w3)
CDP-Diacylglycerol(40:7)

Chemical Formula:

C₅₂H₈₃N₃O₁₅P₂

Weight:

Average: 1052.174
Monoisotopic: 1051.529942025

InChI Key:

DLHOGIVUAZAHPZ-ZDAJIRAHSA-N

InChI:

InChI=1S/C52H83N3O15P2/c1-3-5-7-9-11-13-15-17-19-20-21-22-24-26-28-30-32-34-36-38-48(57)68-44(41-65-47(56)37-35-33-31-29-27-25-23-18-16-14-12-10-8-6-4-2)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/h5,7,11,13-14,16-17,19,21-22,26,28,32,34,39-40,44-45,49-51,58-59H,3-4,6,8-10,12,15,18,20,23-25,27,29-31,33,35-38,41-43H2,1-2H3,(H,61,62)(H,63,64)(H2,53,54,60)/b7-5-,13-11-,16-14-,19-17-,22-21-,28-26-,34-32-/t44-,45-,49+,50?,51-/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-[(4Z,7Z,10Z,13Z,16Z,19Z)-docosa-4,7,10,13,16,19-hexaenoyloxy]-3-[(11Z)-octadec-11-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-[(4Z,7Z,10Z,13Z,16Z,19Z)-docosa-4,7,10,13,16,19-hexaenoyloxy]-3-[(11Z)-octadec-11-enoyloxy]propoxy(hydroxy)phosphoryl]oxy)phosphinic acid

SMILES:

[H][C@@](COC(=O)CCCCCCCCC\C=C/CCCCCC)(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\C=C/C\C=C/C\C=C/C\C=C/C\C=C/C\C=C/CC

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

Physical Properties

State:

Solid

Charge:

-2

Melting point:

Not Available

Experimental Properties:

Property	Value	Source

Predicted Properties

Property	Value	Source
Water Solubility	0.0012 g/L	ALOGPS
logP	7.2	ALOGPS
logP	10.58	ChemAxon
logS	-5.9	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	43	ChemAxon
Refractivity	284.83 m³·mol⁻¹	ChemAxon
Polarizability	113.5 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:

SMPDB Pathways:

phospholipid biosynthesis I (CL(18:2(9Z,12Z)/18:2(9Z,12Z)/18:2(9Z,12Z)/18:2(9Z,12Z)) )

PW001025

KEGG Pathways:

Glycerophospholipid metabolism ec00564

EcoCyc Pathways:

phospholipid biosynthesis I PHOSLIPSYN-PWY

Concentrations

Not Available

Spectra

Spectra:

Spectrum Type	Description	Splash Key
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-03di-1911000100-dc1ee37e2fde63c56aa3	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03di-2910000100-337edb24f107e0c1edb8	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-03di-3921001000-a62eefcbb48f7b4a1cfc	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0bu0-4893000300-8f8ff11f5e952416d16d	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-03e9-7793210020-ef087238d303ee6dfecd	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0bvi-5911000000-fcdd61ca4597f943d858	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0udi-9001000300-eb60448285762a79c357	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-08iu-9071600300-af4dce9fe43bcb10f079	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0a59-7239200510-a367505cf9dfb57fd33b	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0udi-9000000007-38f40e73c9fb6cc6844f	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03fr-3000000009-2870205a025a3949d0ea	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-00dl-0093301003-79787b1ebd133832b29c	View in MoNA
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer

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	HMDB06994
Pubchem Compound ID	53477937
Kegg ID	Not Available
ChemSpider ID	24765834
Wikipedia ID	Not Available
BioCyc ID	Not Available

Enzymes

Protein Details

1. CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase

General function:: Involved in phosphotransferase activity, for other substituted phosphate groups
Specific function:: This protein catalyzes the committed step to the synthesis of the acidic phospholipids
Gene Name:: pgsA
Uniprot ID:: P0ABF8
Molecular weight:: 20700

Reactions

CDP-diacylglycerol + sn-glycerol 3-phosphate = CMP + 3(3-sn-phosphatidyl)-sn-glycerol 1-phosphate.

Protein Details

2. Phosphatidate cytidylyltransferase

General function:: Involved in transferase activity, transferring phosphorus-containing groups
Specific function:: CTP + phosphatidate = diphosphate + CDP- diacylglycerol
Gene Name:: cdsA
Uniprot ID:: P0ABG1
Molecular weight:: 31453

Reactions

CTP + phosphatidate = diphosphate + CDP-diacylglycerol.

Protein Details

3. Protein crcA

General function:: Not Available
Specific function:: Not known; overproduction leads to camphor resistance and chromosome condensation
Gene Name:: crcA
Uniprot ID:: P37001
Molecular weight:: 21770

Protein Details

4. 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
Uniprot ID:: P23830
Molecular weight:: 52801

Reactions

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

Transporters

Protein Details

1. Probable phospholipid ABC transporter-binding protein mlaB

General function:: Involved in phospholipid transporter activity
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:: mlaB
Uniprot ID:: P64602
Molecular weight:: 10680

Protein Details

2. Probable phospholipid ABC transporter-binding protein mlaD

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:: mlaD
Uniprot ID:: P64604
Molecular weight:: 19576

Protein Details

3. 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
Uniprot ID:: P64606
Molecular weight:: 27863

CDP-DG(18:1(11Z)/22:6(4Z,7Z,10Z,13Z,16Z,19Z)) (ECMDB06994) (M2MDB000734)

Structure for #<Compound:0x9fd90108>

Enzymes

Reactions

Reactions

Reactions

Transporters