From August 18th 2026, GtoPdb will require users to register to use the website. Please see our blog post for more information.

chlorogenic acid   Click here for help

GtoPdb Ligand ID: 12477

Synonyms: 3-O-caffeoylquinic acid | caffeoyl quinic acid | chlorogenate
PDB Ligand
Compound class: Natural product
Comment: Chlorogenic acid is a natural product that is present in coffee and black tea and some other plants. Chemically it is a caffeic acid-quinic acid ester. It has been attributed with several biological activities, including antioxidant, anti-carcinogenic and immunomodulatory effects [1-3,5].
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

chlorogenic acid is commercially available from our sponsors

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 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.

✖
Hydrogen bond acceptors 9
Hydrogen bond donors 6
Rotatable bonds 5
Topological polar surface area 164.75
Molecular weight 354.31
XLogP -0.97
No. Lipinski's rules broken 1

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
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.

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/)

✖
Canonical SMILES C1=C(/C=C/C(=O)O[C@@H]2C[C@@](C[C@H]([C@H]2O)O)(C(=O)O)O)C=C(C(=C1)O)O
Isomeric SMILES C1[C@H]([C@H]([C@@H](C[C@@]1(C(=O)O)O)OC(=O)/C=C/C2=CC(=C(C=C2)O)O)O)O
InChI InChI=1S/C16H18O9/c17-9-3-1-8(5-10(9)18)2-4-13(20)25-12-7-16(24,15(22)23)6-11(19)14(12)21/h1-5,11-12,14,17-19,21,24H,6-7H2,(H,22,23)/b4-2+/t11-,12-,14-,16+/m1/s1
InChI Key CWVRJTMFETXNAD-JUHZACGLSA-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. Hibi M. (2023)
Potential of Polyphenols for Improving Sleep: A Preliminary Results from Review of Human Clinical Trials and Mechanistic Insights.
Nutrients, 15 (5). DOI: 10.3390/nu15051257 [PMID:36904255]
2. Lv B, Guo J, Du Y, Chen Y, Zhao X, Yu B, Liu J, Cui T, Mao H, Wang X et al.. (2023)
Chlorogenic acid reduces inflammation by inhibiting the elevated expression of KAT2A to ameliorate lipopolysaccharide-induced acute lung injury.
Br J Pharmacol, 180 (16): 2156-2171. [PMID:36914407]
3. Murai T, Matsuda S. (2023)
The Chemopreventive Effects of Chlorogenic Acids, Phenolic Compounds in Coffee, against Inflammation, Cancer, and Neurological Diseases.
Molecules, 28 (5). DOI: 10.3390/molecules28052381 [PMID:36903626]
4. Sánchez-Alonso P, Griera M, García-Marín J, Rodríguez-Puyol M, Alajarín R, Vaquero JJ, Rodríguez-Puyol D. (2021)
Pyrrolo[1,2-a]quinoxal-5-inium salts and 4,5-dihydropyrrolo[1,2-a]quinoxalines: Synthesis, activity and computational docking for protein tyrosine phosphatase 1B.
Bioorg Med Chem, 44: 116295. [PMID:34246920]
5. Selenge E, Murata T, Kobayashi K, Batkhuu J, Yoshizaki F. (2013)
Flavone tetraglycosides and benzyl alcohol glycosides from the Mongolian medicinal plant Dracocephalum ruyschiana.
J Nat Prod, 76 (2): 186-93. [PMID:23356964]