MiMeDB: Showing metabocard for LysoPC(10:0) (MMDBc0047784)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-19 15:42:29 UTC

Update Date

2022-09-01 01:48:29 UTC

Metabolite ID

MMDBc0047784

Metabolite Identification

Common Name

LysoPC(10:0)

Description

LysoPC(10:0) is a lysophospholipid (LyP). It is a monoglycerophospholipid in which a phosphorylcholine moiety occupies a glycerol substitution site. Lysophosphatidylcholines can have different combinations of fatty acids of varying lengths and saturation attached at the C-1 (sn-1) position. Fatty acids containing 16, 18 and 20 carbons are the most common. LysoPC(10:0), in particular, consists of one decanoyl chain at the C-1 position. Lysophosphatidylcholine is formed by hydrolysis of phosphatidylcholine by the enzyme phospholipase A2, as part of the de-acylation/re-acylation cycle that controls its overall molecular species composition.

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 02231219472D          

 28 27  0  0  1  0            999 V2000
   25.5589  -11.9822    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   26.2764  -11.5683    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   24.8416  -12.3899    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   21.9785  -12.3899    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   25.1453  -11.2652    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   25.9726  -12.6935    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   22.7538  -13.1725    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   21.2671  -11.1545    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   28.4277  -11.9822    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
   27.7107  -11.5683    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   28.0140  -12.6935    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   28.8417  -11.2652    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   29.1450  -12.3899    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   26.9934  -11.9822    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.3982  -11.9822    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.6805  -12.3899    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.1153  -12.3899    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.9635  -11.9822    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.8323  -11.9822    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.2462  -12.3899    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   20.5496  -12.3899    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.5291  -11.9822    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.8121  -12.3899    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   21.2671  -11.9822    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.4073  -12.3899    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   24.1245  -11.9822    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   22.6898  -11.9822    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.1614  -13.1625    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  1  5  1  0  0  0  0
  1  6  2  0  0  0  0
  2 14  1  0  0  0  0
  3 26  1  0  0  0  0
  4 24  1  0  0  0  0
  4 27  1  0  0  0  0
 25  7  1  6  0  0  0
  8 24  2  0  0  0  0
  9 10  1  0  0  0  0
  9 11  1  0  0  0  0
  9 12  1  0  0  0  0
  9 13  1  0  0  0  0
 10 14  1  0  0  0  0
 15 16  1  0  0  0  0
 15 17  1  0  0  0  0
 16 18  1  0  0  0  0
 17 19  1  0  0  0  0
 18 20  1  0  0  0  0
 19 21  1  0  0  0  0
 20 22  1  0  0  0  0
 21 24  1  0  0  0  0
 22 23  1  0  0  0  0
 25 26  1  0  0  0  0
 25 27  1  0  0  0  0
 25 28  1  1  0  0  0
M  CHG  1   9   1
M  END


  Mrv0541 02231219472D          

 28 27  0  0  1  0            999 V2000
   25.5589  -11.9822    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   26.2764  -11.5683    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   24.8416  -12.3899    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   21.9785  -12.3899    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   25.1453  -11.2652    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   25.9726  -12.6935    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   22.7538  -13.1725    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   21.2671  -11.1545    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   28.4277  -11.9822    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
   27.7107  -11.5683    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   28.0140  -12.6935    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   28.8417  -11.2652    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   29.1450  -12.3899    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   26.9934  -11.9822    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.3982  -11.9822    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.6805  -12.3899    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.1153  -12.3899    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.9635  -11.9822    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.8323  -11.9822    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.2462  -12.3899    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   20.5496  -12.3899    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.5291  -11.9822    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.8121  -12.3899    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   21.2671  -11.9822    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.4073  -12.3899    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   24.1245  -11.9822    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   22.6898  -11.9822    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.1614  -13.1625    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  1  5  1  0  0  0  0
  1  6  2  0  0  0  0
  2 14  1  0  0  0  0
  3 26  1  0  0  0  0
  4 24  1  0  0  0  0
  4 27  1  0  0  0  0
 25  7  1  6  0  0  0
  8 24  2  0  0  0  0
  9 10  1  0  0  0  0
  9 11  1  0  0  0  0
  9 12  1  0  0  0  0
  9 13  1  0  0  0  0
 10 14  1  0  0  0  0
 15 16  1  0  0  0  0
 15 17  1  0  0  0  0
 16 18  1  0  0  0  0
 17 19  1  0  0  0  0
 18 20  1  0  0  0  0
 19 21  1  0  0  0  0
 20 22  1  0  0  0  0
 21 24  1  0  0  0  0
 22 23  1  0  0  0  0
 25 26  1  0  0  0  0
 25 27  1  0  0  0  0
 25 28  1  1  0  0  0
M  CHG  1   9   1
M  END
> <DATABASE_ID>
MMDBc0047784

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@@](O)(COC(=O)CCCCCCCCC)COP(O)(=O)OCC[N+](C)(C)C

> <INCHI_IDENTIFIER>
InChI=1S/C18H38NO7P/c1-5-6-7-8-9-10-11-12-18(21)24-15-17(20)16-26-27(22,23)25-14-13-19(2,3)4/h17,20H,5-16H2,1-4H3/p+1/t17-/m1/s1

> <INCHI_KEY>
SECPDKKEUKDCPG-QGZVFWFLSA-O

> <FORMULA>
C18H39NO7P

> <MOLECULAR_WEIGHT>
412.4785

> <EXACT_MASS>
412.246414119

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
45.527164803947564

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
1

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-0.69

> <JCHEM_LOGP>
-1.4746695131384124

> <ALOGPS_LOGS>
-5.15

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.655609236411614

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.8553406136270887

> <JCHEM_PKA_STRONGEST_BASIC>
-3.4040033707844772

> <JCHEM_POLAR_SURFACE_AREA>
102.29000000000002

> <JCHEM_REFRACTIVITY>
115.7894

> <JCHEM_ROTATABLE_BOND_COUNT>
18

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.17e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1-decanoyllysolecithin

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  P   UNK     0      47.710 -22.367   0.000  0.00  0.00           P+0
HETATM    2  O   UNK     0      49.049 -21.594   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      46.371 -23.128   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      41.026 -23.128   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0      46.938 -21.028   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0      48.482 -23.695   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0      42.474 -24.589   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      39.699 -20.822   0.000  0.00  0.00           O+0
HETATM    9  N   UNK     0      53.065 -22.367   0.000  0.00  0.00           N+1
HETATM   10  C   UNK     0      51.727 -21.594   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      52.293 -23.695   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      53.838 -21.028   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      54.404 -23.128   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      50.388 -22.367   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      34.343 -22.367   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      33.004 -23.128   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      35.682 -23.128   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      31.665 -22.367   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      37.020 -22.367   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      30.326 -23.128   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      38.359 -23.128   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      28.988 -22.367   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      27.649 -23.128   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      39.699 -22.367   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      43.694 -23.128   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      45.032 -22.367   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      42.354 -22.367   0.000  0.00  0.00           C+0
HETATM   28  H   UNK     0      45.101 -24.570   0.000  0.00  0.00           H+0
CONECT    1    2    3    5    6                                             
CONECT    2    1   14                                                       
CONECT    3    1   26                                                       
CONECT    4   24   27                                                       
CONECT    5    1                                                            
CONECT    6    1                                                            
CONECT    7   25                                                            
CONECT    8   24                                                            
CONECT    9   10   11   12   13                                             
CONECT   10    9   14                                                       
CONECT   11    9                                                            
CONECT   12    9                                                            
CONECT   13    9                                                            
CONECT   14    2   10                                                       
CONECT   15   16   17                                                       
CONECT   16   15   18                                                       
CONECT   17   15   19                                                       
CONECT   18   16   20                                                       
CONECT   19   17   21                                                       
CONECT   20   18   22                                                       
CONECT   21   19   24                                                       
CONECT   22   20   23                                                       
CONECT   23   22                                                            
CONECT   24    4    8   21                                                  
CONECT   25    7   26   27   28                                             
CONECT   26    3   25                                                       
CONECT   27    4   25                                                       
CONECT   28   25                                                            
MASTER        0    0    0    0    0    0    0    0   28    0   54    0
END

Synonyms

Value	Source
1-Capryl-2-lysophosphatidylcholine	HMDB
1-Capryl-L-alpha-phosphorylcholine	HMDB
1-Decanoyl-sn-glycero-3-phosphocholine	HMDB
1-Decanoyl-sn-glycerol-3-phosphorylcholine	HMDB
1-Decanoyllysolecithin	HMDB
Decanoyl lysolecithin	HMDB
LPC(10:0/0:0)	HMDB
LyPC(10:0)	HMDB
LyPC(10:0/0:0)	HMDB
Lysophosphatidylcholine(10:0)	HMDB
Lysophosphatidylcholine(10:0/0:0)	HMDB
LysoPIC(10:0/0:0)	HMDB
1-Animal fats-glycero-3-phosphocholine	HMDB
LPC(10:0)	HMDB
1-Decanoic acid-glycero-3-phosphocholine	HMDB
LysoPC(10:0)	HMDB
LysoPC(10:0/0:0)	Lipid Annotator, HMDB
1-Decanoylglycerophosphocholine	HMDB

Molecular Formula

C₁₈H₃₉NO₇P

Average Mass

412.4785

Monoisotopic Mass

412.246414119

IUPAC Name

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

Traditional Name

1-decanoyllysolecithin

CAS Registry Number

Not Available

SMILES

[H][C@@](O)(COC(=O)CCCCCCCCC)COP(O)(=O)OCC[N+](C)(C)C

InChI Identifier

InChI=1S/C18H38NO7P/c1-5-6-7-8-9-10-11-12-18(21)24-15-17(20)16-26-27(22,23)25-14-13-19(2,3)4/h17,20H,5-16H2,1-4H3/p+1/t17-/m1/s1

InChI Key

SECPDKKEUKDCPG-QGZVFWFLSA-O

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 1-acyl-sn-glycero-3-phosphocholines. These are glycerophosphocholines in which the glycerol is esterified with a fatty acid at O-1 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

1-acyl-sn-glycero-3-phosphocholines

Alternative Parents

Substituents

1-acyl-sn-glycero-3-phosphocholine
Phosphocholine
Fatty acid ester
Dialkyl phosphate
Organic phosphoric acid derivative
Phosphoric acid ester
Fatty acyl
Alkyl phosphate
Tetraalkylammonium salt
Quaternary ammonium salt
Carboxylic acid ester
Secondary alcohol
Monocarboxylic acid or derivatives
Carboxylic acid derivative
Organic salt
Hydrocarbon derivative
Organic oxide
Organooxygen compound
Organonitrogen compound
Organopnictogen 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

Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.0032 g/L	ALOGPS
logP	-0.69	ALOGPS
logP	-1.5	ChemAxon
logS	-5.2	ALOGPS
pKa (Strongest Acidic)	1.86	ChemAxon
pKa (Strongest Basic)	-3.4	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	18	ChemAxon
Refractivity	115.79 m³·mol⁻¹	ChemAxon
Polarizability	45.53 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	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-001j-1901000000-6ee90c0e03e31951c3c6	2016-09-22	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positive	splash10-000b-9822100000-046702be899a541da73d	2017-10-06	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , positive	splash10-0f8i-2900100000-df21f3ae5cf3289a7a27	2017-09-14	View Spectrum

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

Metabolic Reactions

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
Eukaryota/Fungi	Ascomycota	1	Human feces; Human saliva	Unknown

Exposure Sources

Source Type	Activity	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

HMDB0003752

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB023221

KNApSAcK ID

Not Available

Chemspider ID

4473396

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5313971

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Wishart DS, Li C, Marcu A, Badran H, Pon A, Budinski Z, Patron J, Lipton D, Cao X, Oler E, Li K, Paccoud M, Hong C, Guo AC, Chan C, Wei W, Ramirez-Gaona M: PathBank: a comprehensive pathway database for model organisms. Nucleic Acids Res. 2020 Jan 8;48(D1):D470-D478. doi: 10.1093/nar/gkz861. [PubMed:31602464 ]

Showing metabocard for LysoPC(10:0) (MMDBc0047784)

MOL for #<Metabolite:0x00007f53b95a61a8>

3D MOL for #<Metabolite:0x00007f53b95a61a8>

3D SDF for #<Metabolite:0x00007f53b95a61a8>

3D-SDF for #<Metabolite:0x00007f53b95a61a8>

PDB for #<Metabolite:0x00007f53b95a61a8>

3D PDB for #<Metabolite:0x00007f53b95a61a8>

SMILES for #<Metabolite:0x00007f53b95a61a8>

INCHI for #<Metabolite:0x00007f53b95a61a8>

Structure for #<Metabolite:0x00007f53b95a61a8>

3D Structure for #<Metabolite:0x00007f53b95a61a8>