clonidine   Click here for help

GtoPdb Ligand ID: 516

Synonyms: Catapres® | Kapvay®
Approved drug PDB Ligand
clonidine is an approved drug (FDA (1974))
Compound class: Synthetic organic
Comment: Clonidine is an α2 adrenoceptor agonist.
The structure shown here is in the amino form. A tautomeric imino form, represented by CHEBI:3757 also exists.
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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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View more information in the IUPHAR Pharmacology Education Project: clonidine

clonidine is commercially available from our sponsors

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 3
Hydrogen bond donors 2
Rotatable bonds 2
Topological polar surface area 36.42
Molecular weight 229.02
XLogP 2.68
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 Clc1cccc(c1NC1=NCCN1)Cl
Isomeric SMILES Clc1cccc(c1NC1=NCCN1)Cl
InChI InChI=1S/C9H9Cl2N3/c10-6-2-1-3-7(11)8(6)14-9-12-4-5-13-9/h1-3H,4-5H2,(H2,12,13,14)
InChI Key GJSURZIOUXUGAL-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. Jasper JR, Lesnick JD, Chang LK, Yamanishi SS, Chang TK, Hsu SA, Daunt DA, Bonhaus DW, Eglen RM. (1998)
Ligand efficacy and potency at recombinant alpha2 adrenergic receptors: agonist-mediated [35S]GTPgammaS binding.
Biochem Pharmacol, 55 (7): 1035-43. [PMID:9605427]
2. Knaus A, Zong X, Beetz N, Jahns R, Lohse MJ, Biel M, Hein L. (2007)
Direct inhibition of cardiac hyperpolarization-activated cyclic nucleotide-gated pacemaker channels by clonidine.
Circulation, 115 (7): 872-80. [PMID:17261653]
3. Kurko D, Kapui Z, Nagy J, Lendvai B, Kolok S. (2014)
Analysis of functional selectivity through G protein-dependent and -independent signaling pathways at the adrenergic α(2C) receptor.
Brain Res Bull, 107: 89-101. [PMID:25080296]
4. Minneman KP, Theroux TL, Hollinger S, Han C, Esbenshade TA. (1994)
Selectivity of agonists for cloned alpha 1-adrenergic receptor subtypes.
Mol Pharmacol, 46 (5): 929-36. [PMID:7969082]
5. Peltonen JM, Pihlavisto M, Scheinin M. (1998)
Subtype-specific stimulation of [35S]GTPgammaS binding by recombinant alpha2-adrenoceptors.
Eur J Pharmacol, 355 (2-3): 275-9. [PMID:9760042]
6. Pihlavisto M, Sjöholm B, Scheinin M, Wurster S. (1998)
Modulation of agonist binding to recombinant human alpha2-adrenoceptors by sodium ions.
Biochim Biophys Acta, 1448 (1): 135-46. [PMID:9824686]
7. Proudman RGW, Akinaga J, Baker JG. (2022)
The signaling and selectivity of α-adrenoceptor agonists for the human α2A, α2B and α2C-adrenoceptors and comparison with human α1 and β-adrenoceptors.
Pharmacol Res Perspect, 10 (5): e01003. [PMID:36101495]
8. Proudman RGW, Baker JG. (2021)
The selectivity of α-adrenoceptor agonists for the human α1A, α1B, and α1D-adrenoceptors.
Pharmacol Res Perspect, 9 (4): e00799. [PMID:34355529]
9. Zhang L, Schaner ME, Giacomini KM. (1998)
Functional characterization of an organic cation transporter (hOCT1) in a transiently transfected human cell line (HeLa).
J Pharmacol Exp Ther, 286 (1): 354-61. [PMID:9655880]