MiMeDB: Showing metabocard for 2-Acylglycerophosphocholine (MMDBc0029754)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-17 23:40:15 UTC

Update Date

2022-08-31 17:16:40 UTC

Metabolite ID

MMDBc0029754

Metabolite Identification

Common Name

2-Acylglycerophosphocholine

Description

2-acylglycerophosphocholine belongs to the class of Lysophosphatidylcholines. These are glycerophosphocholines (molecules containing a choline moiety attached to the phosphate group linked to a glycerol) in which the glycerol is attached to one saturated fatty acid each through an ester linkage. (inferred from compound structure)2-acyl-sn-glycero-3-phosphocholines are a class of phospholipids that are intermediates in the metabolism of lipids. Because they result from the hydrolysis of an acyl group from the sn-1 position of phosphatidylcholine, they are also called 1-lysophosphatidylcholine (or 1-lysoPC, in short). The synthesis of phosphatidylcholines with specific fatty acids occurs through the synthesis of 1-lysoPC. The formation of various other lipids generates 1-lysoPC as a by-product. Other synonyms for this class of compounds are 2-acylglycero-3-phosphocholine, 1-lyso-2-acyl-sn-glycero-3-phosphocholine, Œ≤-lysophosphatidylcholine, 2-acylglycerophosphocholine, L-1-lysolecithin and 1-lecithin. (WikiPedia)

Structure

MOL SDF PDB SMILES InChI

Structure #1
  Mrv0541 02241206282D          

 18 17  0  0  0  0            999 V2000
   -4.8908    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7638   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5888    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4618    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7474    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1105    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2539    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1763    0.4125    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    0.1105   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9684    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7309   -0.3020    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9059    1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5395    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0329    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6039    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3184    0.4125    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
  1 10  1  0  0  0  0
  2 10  1  0  0  0  0
  3 10  1  0  0  0  0
  4  5  1  0  0  0  0
  4 10  1  0  0  0  0
  5 16  1  0  0  0  0
  6  9  1  0  0  0  0
  6 11  1  0  0  0  0
  7  9  1  0  0  0  0
  7 17  1  0  0  0  0
  8 12  2  0  0  0  0
  8 15  1  0  0  0  0
  9 15  1  0  0  0  0
 13 18  2  0  0  0  0
 14 18  1  0  0  0  0
 16 18  1  0  0  0  0
 17 18  1  0  0  0  0
M  CHG  1  10   1
M  END
> <DATABASE_ID>
MMDBc0029754

> <DATABASE_NAME>
MIME

> <SMILES>
C[N+](C)(C)CCOP(O)(=O)OCC(CO)OC=O

> <INCHI_IDENTIFIER>
InChI=1S/C9H20NO7P/c1-10(2,3)4-5-16-18(13,14)17-7-9(6-11)15-8-12/h8-9,11H,4-7H2,1-3H3/p+1

> <INCHI_KEY>
WOBXACRJIURDTO-UHFFFAOYSA-O

> <FORMULA>
C9H21NO7P

> <MOLECULAR_WEIGHT>
286.2393

> <EXACT_MASS>
286.105563543

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
26.933196369911713

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[2-(formyloxy)-3-hydroxypropoxy][2-(trimethylazaniumyl)ethoxy]phosphinic acid

> <ALOGPS_LOGP>
-2.28

> <JCHEM_LOGP>
-5.3358847231384114

> <ALOGPS_LOGS>
-2.23

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.579761911929722

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.8550633573025026

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9835377822086526

> <JCHEM_POLAR_SURFACE_AREA>
102.29

> <JCHEM_REFRACTIVITY>
74.465

> <JCHEM_ROTATABLE_BOND_COUNT>
10

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.91e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-(formyloxy)-3-hydroxypropoxy(2-(trimethylammonio)ethoxy)phosphinic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: Structure #1                                      
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0      -9.129   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -7.026  -0.564   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -8.566   2.104   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -6.462   1.540   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -5.128   0.770   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.540  -1.540   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.206   0.770   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.207   0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0      -7.796   0.770   0.000  0.00  0.00           N+1
HETATM   11  O   UNK     0       0.206  -2.310   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       5.541   0.770   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      -3.231  -0.564   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0      -1.691   2.104   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       2.874   0.770   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0      -3.795   1.540   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0      -1.127   0.000   0.000  0.00  0.00           O+0
HETATM   18  P   UNK     0      -2.461   0.770   0.000  0.00  0.00           P+0
CONECT    1   10                                                            
CONECT    2   10                                                            
CONECT    3   10                                                            
CONECT    4    5   10                                                       
CONECT    5    4   16                                                       
CONECT    6    9   11                                                       
CONECT    7    9   17                                                       
CONECT    8   12   15                                                       
CONECT    9    6    7   15                                                  
CONECT   10    1    2    3    4                                             
CONECT   11    6                                                            
CONECT   12    8                                                            
CONECT   13   18                                                            
CONECT   14   18                                                            
CONECT   15    8    9                                                       
CONECT   16    5   18                                                       
CONECT   17    7   18                                                       
CONECT   18   13   14   16   17                                             
MASTER        0    0    0    0    0    0    0    0   18    0   34    0
END

Synonyms

Value	Source
[2-(Formyloxy)-3-hydroxypropoxy][2-(trimethylazaniumyl)ethoxy]phosphinate	Generator

Molecular Formula

C₉H₂₁NO₇P

Average Mass

286.2393

Monoisotopic Mass

286.105563543

IUPAC Name

[2-(formyloxy)-3-hydroxypropoxy][2-(trimethylazaniumyl)ethoxy]phosphinic acid

Traditional Name

2-(formyloxy)-3-hydroxypropoxy(2-(trimethylammonio)ethoxy)phosphinic acid

CAS Registry Number

Not Available

SMILES

C[N+](C)(C)CCOP(O)(=O)OCC(CO)OC=O

InChI Identifier

InChI=1S/C9H20NO7P/c1-10(2,3)4-5-16-18(13,14)17-7-9(6-11)15-8-12/h8-9,11H,4-7H2,1-3H3/p+1

InChI Key

WOBXACRJIURDTO-UHFFFAOYSA-O

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 2-acyl-sn-glycero-3-phosphocholines. These are glycerophosphocholines in which the glycerol is esterified with a fatty acid at O-2 position, and linked at position 3 to a phosphocholine.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Glycerophospholipids

Sub Class

Glycerophosphocholines

Direct Parent

2-acyl-sn-glycero-3-phosphocholines

Alternative Parents

Substituents

2-acyl-sn-glycero-3-phosphocholine
Phosphocholine
Dialkyl phosphate
Organic phosphoric acid derivative
Phosphoric acid ester
Alkyl phosphate
Tetraalkylammonium salt
Quaternary ammonium salt
Carboxylic acid ester
Monocarboxylic acid or derivatives
Carboxylic acid derivative
Organic salt
Hydrocarbon derivative
Primary alcohol
Organic oxide
Organopnictogen compound
Organooxygen compound
Organonitrogen compound
Organic oxygen compound
Organic nitrogen compound
Carbonyl group
Amine
Alcohol
Organic cation
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	1.91 g/L	ALOGPS
logP	-2.3	ALOGPS
logP	-5.3	ChemAxon
logS	-2.2	ALOGPS
pKa (Strongest Acidic)	1.86	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	102.29 Å²	ChemAxon
Rotatable Bond Count	10	ChemAxon
Refractivity	74.46 m³·mol⁻¹	ChemAxon
Polarizability	26.93 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Spectrum Type	Description	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	2022-08-20	View Spectrum

Chromatographic Retention Times and Retention Indices

Retention Times

Chromatography Type	Technique	Column	Deposition Date	Retention Time (s)
Liquid Chromatography	HILIC	Waters Acquity UPLC-BEH Amide column (eluted)	2025-10-23	576.7
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (eluted)	2025-10-23	449.6
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (eluted)	2025-10-23	53.3
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-23	277.0
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-23	235.6
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (eluted)	2025-10-23	232.2
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	392.6
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-23	920.4
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-23	451.3
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	152.7
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-23	366.8
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	167.6
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	75.1
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-23	355.7
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-23	654.1
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	46.8
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	223.8
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-23	851.2
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-23	610.5

Retention Indices

Chromatography Type	Peak Label	SMILES	Stationary Phase	Deposition Date	Retention Index
Gas Chromatography	2-Acylglycerophosphocholine_TMS_1	C[N+](C)(C)CCOP(=O)(O)OCC(CO[Si](C)(C)C)OC=O	standard non polar	2025-10-23	2205.52
Gas Chromatography	2-Acylglycerophosphocholine_TMS_2	C[N+](C)(C)CCOP(=O)(OCC(CO)OC=O)O[Si](C)(C)C	standard non polar	2025-10-23	2419.59
Gas Chromatography	2-Acylglycerophosphocholine_TMS_3	C[N+](C)(C)CCOP(=O)(OCC(CO[Si](C)(C)C)OC=O)O[Si](C)(C)C	standard non polar	2025-10-23	2215.87
Gas Chromatography	2-Acylglycerophosphocholine_TMS_1	C[N+](C)(C)CCOP(=O)(O)OCC(CO[Si](C)(C)C)OC=O	standard polar	2025-10-23	2290.31
Gas Chromatography	2-Acylglycerophosphocholine_TMS_2	C[N+](C)(C)CCOP(=O)(OCC(CO)OC=O)O[Si](C)(C)C	standard polar	2025-10-23	1737.2
Gas Chromatography	2-Acylglycerophosphocholine_TMS_3	C[N+](C)(C)CCOP(=O)(OCC(CO[Si](C)(C)C)OC=O)O[Si](C)(C)C	standard polar	2025-10-23	1747.47

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Microbial Pathways

Pathways

Not Available

Metabolic Reactions

Reactions

This table shows at most 20 reactions. For the full list of associated reactions:

See All Associated Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria/Eubacteria	Proteobacteria	1	Human ; Human feces; Human feces; pleural fluid plaque; bal	Unknown

Exposure Sources

Other Exposures

Source Type	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

24798686

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

Keseler IM, 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 AG, Mackie A, Paulsen I, Gunsalus RP, Karp PD: EcoCyc: a comprehensive database of Escherichia coli biology. Nucleic Acids Res. 2011 Jan;39(Database issue):D583-90. doi: 10.1093/nar/gkq1143. Epub 2010 Nov 21. [PubMed:21097882 ]
Kanehisa M, Goto S, Sato Y, Furumichi M, Tanabe M: KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res. 2012 Jan;40(Database issue):D109-14. doi: 10.1093/nar/gkr988. Epub 2011 Nov 10. [PubMed:22080510 ]
Authors unspecified: Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res. 2012 Jan;40(Database issue):D71-5. doi: 10.1093/nar/gkr981. Epub 2011 Nov 18. [PubMed:22102590 ]

Showing metabocard for 2-Acylglycerophosphocholine (MMDBc0029754)

MOL for #<Metabolite:0x00007f9ab4e6eca8>

3D MOL for #<Metabolite:0x00007f9ab4e6eca8>

3D SDF for #<Metabolite:0x00007f9ab4e6eca8>

3D-SDF for #<Metabolite:0x00007f9ab4e6eca8>

PDB for #<Metabolite:0x00007f9ab4e6eca8>

3D PDB for #<Metabolite:0x00007f9ab4e6eca8>

SMILES for #<Metabolite:0x00007f9ab4e6eca8>

INCHI for #<Metabolite:0x00007f9ab4e6eca8>

Structure for #<Metabolite:0x00007f9ab4e6eca8>

3D Structure for #<Metabolite:0x00007f9ab4e6eca8>