agmatine   Click here for help

GtoPdb Ligand ID: 4127

PDB Ligand
Compound class: Metabolite
Comment: Agmatine is proposed as an endogenous ligand of I2 imidazoline binding sites [1-4] with neurotransmitter-like action [6]. It is synthesised in the brain from L-arginine and is an intermediate in polyamine biosynthesis [7]. Agmatine is also produced as a metabolite by the human commensal microbe Bacteroides vulgatus.
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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
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 Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/). 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 4
Hydrogen bond donors 3
Rotatable bonds 4
Topological polar surface area 90.42
Molecular weight 130.12
XLogP -0.9
No. Lipinski's rules broken 0

Generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/)
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.

Generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/)

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Canonical SMILES NCCCCN=C(N)N
Isomeric SMILES NCCCCN=C(N)N
InChI InChI=1S/C5H14N4/c6-3-1-2-4-9-5(7)8/h1-4,6H2,(H4,7,8,9)
InChI Key QYPPJABKJHAVHS-UHFFFAOYSA-N

Generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/)
References
1. Halaris A, Plietz J. (2007)
Agmatine : metabolic pathway and spectrum of activity in brain.
CNS Drugs, 21 (11): 885-900. [PMID:17927294]
2. Herman ZS. (1997)
Agmatine--a novel endogenous ligand of imidazoline receptors.
Pol J Pharmacol, 49 (2-3): 85-8. [PMID:9437754]
3. Hudson AL, Luscombe S, Gouch RE, Nutt DJ, Tyacke RJ. (1999)
Endogenous indoleamines demonstrate moderate affinity for I2 binding sites.
Ann N Y Acad Sci, 881: 212-6. [PMID:10415919]
4. Li G, Regunathan S, Barrow CJ, Eshraghi J, Cooper R, Reis DJ. (1994)
Agmatine: an endogenous clonidine-displacing substance in the brain.
Science, 263 (5149): 966-9. [PMID:7906055]
5. Li WG, Yu Y, Zhang ZD, Cao H, Xu TL. (2010)
ASIC3 channels integrate agmatine and multiple inflammatory signals through the nonproton ligand sensing domain.
Mol Pain, 6: 88. [PMID:21143836]
6. Reis DJ, Regunathan S. (1999)
Agmatine: an endogenous ligand at imidazoline receptors is a novel neurotransmitter.
Ann N Y Acad Sci, 881: 65-80. [PMID:10415899]
7. Reis DJ, Regunathan S. (2000)
Is agmatine a novel neurotransmitter in brain?.
Trends Pharmacol Sci, 21 (5): 187-93. [PMID:10785653]
8. Yun C, Yan S, Liao B, Ding Y, Qi X, Zhao M, Wang K, Zhuo Y, Nie Q, Ye C et al.. (2024)
The microbial metabolite agmatine acts as an FXR agonist to promote polycystic ovary syndrome in female mice.
Nat Metab, 6 (5): 947-962. [PMID:38769396]
9. Zhu MY, Iyo A, Piletz JE, Regunathan S. (2004)
Expression of human arginine decarboxylase, the biosynthetic enzyme for agmatine.
Biochim Biophys Acta, 1670 (2): 156-64. [PMID:14738999]