glycine   Click here for help

GtoPdb Ligand ID: 727

PDB Ligand
Compound class: Metabolite or derivative
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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.

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View interactive charts of activity data across species

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2D Structure
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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.

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Physico-chemical Properties
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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.

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Hydrogen bond acceptors 3
Hydrogen bond donors 2
Rotatable bonds 1
Topological polar surface area 63.32
Molecular weight 75.03
XLogP -3.35
No. Lipinski's rules broken 0
SMILES / InChI / InChIKey
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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.

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Canonical SMILES NCC(=O)O
Isomeric SMILES NCC(=O)O
InChI InChI=1S/C2H5NO2/c3-1-2(4)5/h1,3H2,(H,4,5)
InChI Key DHMQDGOQFOQNFH-UHFFFAOYSA-N
Bioactivity Comments
Glycine has been described as a coagonist with L-glutamic acid of NMDA receptors [4].
Natural/Endogenous Targets
Target
GluN1
GluN2A
GluN2B
GluN2C
GluN2D
Glycine Receptor (All subtypes)
glycine receptor α1 subunit
glycine receptor α2 subunit
glycine receptor α3 subunit
glycine receptor α4 subunit (pseudogene in humans)
glycine receptor β subunit
GPRC6 receptor
Enzymes Catalysing Reactions with this Compound as a Substrate or Product
Enzyme EC number Reaction Reference
Dipeptidase 1 3.4.13.19 LTD4 + H2O = LTE4 + glycine
Dipeptidase 2 3.4.13.19 LTD4 + H2O = LTE4 + glycine
Transporters Moving this Compound Across a Lipid Membrane
Transporter EC number Reaction Reference
GlyT1
GlyT2
Vesicular inhibitory amino acid transporter
Proton-coupled Amino acid Transporter 1 9
Proton-coupled Amino acid Transporter 2
Alanine/serine/cysteine transporter 2
B0AT1 3
B0AT2 3
B0AT3 10
NTT4 12
sodium-coupled neutral amino acid transporter 1 1
sodium-coupled neutral amino acid transporter 2 6
sodium-coupled neutral amino acid transporter 4 5
Sodium-coupled neutral amino acid transporter 5 8
Selectivity at GPCRs
Key to terms and symbols Click column headers to sort
Target Sp. Type Action Value Parameter Concentration range (M) Reference
GPRC6 receptor Ligand is endogenous in the given species Hs Agonist Full agonist 3.6 pEC50 - 11
⤷ pEC50 3.6 [11]
Selectivity at ion channels
Key to terms and symbols Click column headers to sort
Target Sp. Type Action Value Parameter Concentration range (M) Reference
Glycine Receptor (All subtypes) Ligand is endogenous in the given species Hs Agonist Agonist 4.3 – 4.6 pEC50 - 2,7
⤷ pEC50 4.3 – 4.6 [2,7]
GluN1 Ligand is endogenous in the given species Hs Agonist Agonist - - -
⤷ [Binds to: glycine site]
GluN2A Ligand is endogenous in the given species Hs Agonist Agonist - - -
⤷ [Binds to: glycine site] GluN2D > GluN2C > GluN2B > GluN2A
GluN2B Ligand is endogenous in the given species Hs Agonist Agonist - - -
⤷ [Binds to: glycine site] GluN2D > GluN2C > GluN2B > GluN2A
GluN2C Ligand is endogenous in the given species Hs Agonist Agonist - - -
⤷ [Binds to: glycine site] GluN2D > GluN2C > GluN2B > GluN2A
GluN2D Ligand is endogenous in the given species Hs Agonist Agonist - - -
⤷ [Binds to: glycine site] GluN2D > GluN2C > GluN2B > GluN2A
Additional information and targets (data relate to human unless otherwise stated)
Description Data Reference
Selective agonists (potency order) at glycine receptor α3 subunit glycine > β-alanine > taurine
Selective agonists (potency order) at glycine receptor α1 subunit glycine > β-alanine > taurine
Selective agonists (potency order) at glycine receptor α2 subunit glycine > β-alanine > taurine
Endogenous substrates at Alanine/serine/cysteine transporter 2 L-alanine = L-serine = L-cysteine (low Vmax) = L-threonine = L-glutamine = L-asparagine >> L-methionine ≅ glycine ≅ L-leucine > L-valine > L-glutamic acid (enhanced at low pH)
Endogenous substrates at B0AT1 L-leucine, L-methionine, L-isoleucine, L-valine > L-asparagine, L-phenylalanine, L-alanine, L-serine > L-threonine, glycine, L-proline 3
Endogenous substrates at B0AT2 L-proline > L-alanine, L-valine, L-methionine, L-leucine > L-isoleucine, L-threonine, L-asparagine, L-serine, L-phenylalanine > glycine 3
Endogenous substrates at B0AT3 L-alanine, glycine > L-methionine, L-phenylalanine, L-leucine, L-histidine, L-glutamine 10
Endogenous substrates at NTT4 L-leucine, L-methionine, L-proline > L-cysteine, L-alanine, L-glutamine, L-serine > L-histidine, glycine 12
Substrates at sodium-coupled neutral amino acid transporter 2 L-alanine, L-methionine > L-asparagine, L-glutamine, L-serine, L-proline, glycine > L-threonine, L-leucine, L-phenylalanine 6
Substrates at sodium-coupled neutral amino acid transporter 4 L-histidine > L-arginine, L-alanine, L-asparagine, L-lysine > glycine, L-glutamine, L-serine, L-proline, L-leucine, L-phenylalanine 5
Substrates at Sodium-coupled neutral amino acid transporter 5 L-asparagine, L-serine, L-histidine, L-glutamine > glycine, L-alanine 8
Substrates at sodium-coupled neutral amino acid transporter 1 L-alanine > L-serine, L-glutamine, L-asparagine, L-histidine, L-cysteine, L-methionine > glycine, L-threonine, L-proline, L-tyrosine, L-valine 1
Ligand mentioned in the following text fields
Glycine transporter subfamily overview
Leukotriene and lipoxin metabolism overview
SLC32 vesicular inhibitory amino acid transporter overview
SLC6 neurotransmitter transporter family overview
Glycine transporter subfamily comments
Ionotropic glutamate receptors comments
SLC7 family comments