lysophosphatidylcholine   Click here for help

GtoPdb Ligand ID: 2508

Abbreviated name: LPC
Compound class: Metabolite
Comment: The structure shown here is a representative example of the lysophosphatidylcholine class of compounds. The R group terminal linked to the ester (shown here as a methyl group) is a fatty acid chain of varying length. For examples of lysophospatidylcholine compounds with specified chain lengths see oleoyl-lysophosphatidylcholine and 1-palmitoyl-lysophosphatidylcholine.
Click here for help

Ligand Activity Visualisation Charts

These are box plot that provide a unique visualisation, summarising all the activity data for a ligand taken from ChEMBL and GtoPdb across multiple targets and species. Click on a plot to see the median, interquartile range, low and high data points. A value of zero indicates that no data are available. A separate chart is created for each target, and where possible the algorithm tries to merge ChEMBL and GtoPdb targets by matching them on name and UniProt accession, for each available species. However, please note that inconsistency in naming of targets may lead to data for the same target being reported across multiple charts.

✖

View interactive charts of activity data across species
2D Structure
Click here for help

2D Structure

An image of the ligand's 2D structure. For small molecules with SMILES these are drawn using the NCI/CADD Chemical Identifier Resolver. Click on the image to access the chemical structure search tool with the ligand pre-loaded in the structure editor. For other types of ligands, e.g. longer nucleotides and peptides, a manually drawn representation of the molecule may be provided.

✖
Click here for structure editor
Physico-chemical Properties
Click here for help

Physico-chemical Properties

Calculated molecular properties are available for small molecules and natural products (not peptides). Properties were generated using the CDK toolkit. All properties were selected to enable the prediction of the Lipinski Rule-of-Five profile or ‘druglikeness’ for each ligand. For more info on each category see the help pages.

✖
Hydrogen bond acceptors 7
Hydrogen bond donors 1
Rotatable bonds 10
Topological polar surface area 114.93
Molecular weight 299.11
XLogP -2.19
No. Lipinski's rules broken 0
SMILES / InChI / InChIKey
Click here for help

SMILES / InChI / InChIKey

SMILES (Simplified Molecular Input Line Entry Specification) A specification for unambiguously describing the structure of chemical molecules using short ASCII strings. Canonical SMILES specify a unique representation of the 2D structure without chiral or isotopic specifications. Isomeric SMILES include chiral specification and isotopes.

Standard InChI (IUPAC International Chemical Identifier) and InChIKey InChI is a non-proprietary, standard, textual identifier for chemical substances designed to facilitate linking of information and database searching. An InChIKey is a simplified version of a full InChI, designed for easier web searching.

✖
Canonical SMILES OC(COP(=O)(OCC[N+](C)(C)C)[O-])COC(=O)C
Isomeric SMILES O[C@@H](COP(=O)(OCC[N+](C)(C)C)[O-])COC(=O)C
InChI InChI=1S/C10H22NO7P/c1-9(12)16-7-10(13)8-18-19(14,15)17-6-5-11(2,3)4/h10,13H,5-8H2,1-4H3/t10-/m1/s1
InChI Key RYCNUMLMNKHWPZ-SNVBAGLBSA-N
Selectivity at ion channels
Key to terms and symbols Click column headers to sort
Target Sp. Type Action Value Parameter Concentration range (M) Reference
TRPV2 Mm Activator Activation - - 1x10-6 6-7
⤷ Conc range: 1x10-6 M [6-7]
ASIC3 Ligand is endogenous in the given species Hs Activator Partial agonist 5.4 pEC50 - 5
⤷ pEC50 5.4 (EC50 3.981x10-6 M) [5]
TRPC5 Ligand is endogenous in the given species Hs Activator - - - -
⤷
TRPC6 Ligand is endogenous in the given species Hs Activator - - - -
⤷
K2P10.1 Hs Activator - - - - 4
⤷ [4]
Targets where the ligand is described in the comment field
Target Comment
GPR4 An initial report suggesting activation by lysophosphatidylcholine and sphingosylphosphorylcholine [13] has been retracted [8]. GPR4, GPR65, GPR68 and GPR132 are now thought to function as proton-sensing receptors detecting acidic pH [2,9]. Gene disruption is associated with increased perinatal mortality and impaired vascular proliferation [12]. Negative allosteric modulators of GPR4 have been reported [10].
GPR132 GPR4, GPR65, GPR68 and GPR132 are now thought to function as proton-sensing receptors detecting acidic pH [2,9]. Reported to respond to lysophosphatidylcholine [3], but later retracted [11].
autotaxin Autotaxin is an extracellular multifunctional enzyme. Its lysophospholipase D activity hydrolyzes lysophosphatidylcholine to form the bioactive lipid lysophosphatidic acid (LPA). Autotaxin is considered to be the main source of LPA in vivo. It also acts on other substrates to produce additional bioactive lipids, for example generating sphingosine-1-phosphate (S1P) from sphingosylphosphorylcholine [1].
Ligand mentioned in the following text fields
Phospholipase A2 overview
Platelet-activating factor receptor overview
Phosphatidylcholine-specific phospholipase D comments