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cordycepin   Click here for help

GtoPdb Ligand ID: 4630

Synonyms: 3'-deoxyadenosine
PDB Ligand
Compound class: Natural product
Comment: Cordycepin is a biologically active adenosine analogue isolated from Ophiocordyceps (cordyceps) species fungi (e.g. O. militaris and O. sinensis) [6].

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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 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 7
Hydrogen bond donors 3
Rotatable bonds 2
Topological polar surface area 119.31
Molecular weight 251.1
XLogP -1.25
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 OCC1CC(C(O1)n1cnc2c1ncnc2N)O
Isomeric SMILES OC[C@@H]1C[C@H]([C@@H](O1)n1cnc2c1ncnc2N)O
InChI InChI=1S/C10H13N5O3/c11-8-7-9(13-3-12-8)15(4-14-7)10-6(17)1-5(2-16)18-10/h3-6,10,16-17H,1-2H2,(H2,11,12,13)/t5-,6+,10+/m0/s1
InChI Key OFEZSBMBBKLLBJ-BAJZRUMYSA-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. Baldwin SA, Yao SY, Hyde RJ, Ng AM, Foppolo S, Barnes K, Ritzel MW, Cass CE, Young JD. (2005)
Functional characterization of novel human and mouse equilibrative nucleoside transporters (hENT3 and mENT3) located in intracellular membranes.
J Biol Chem, 280 (16): 15880-7. [PMID:15701636]
2. Chen YY, Chen CH, Lin WC, Tung CW, Chen YC, Yang SH, Huang BM, Chen RJ. (2021)
The Role of Autophagy in Anti-Cancer and Health Promoting Effects of Cordycepin.
Molecules, 26 (16). [PMID:34443541]
3. Jiao L, Yu Z, Zhong X, Yao W, Xing L, Ma G, Shen J, Wu Y, Du K, Liu J et al.. (2023)
Cordycepin improved neuronal synaptic plasticity through CREB-induced NGF upregulation driven by MG-M2 polarization: a microglia-neuron symphony in AD.
Biomed Pharmacother, 157: 114054. [PMID:36462314]
4. Soraksa N, Heebkaew N, Promjantuek W, Kunhorm P, Kaokean P, Chaicharoenaudomung N, Noisa P. (2024)
Cordycepin, a bioactive compound from Cordyceps spp., moderates Alzheimer's disease-associated pathology via anti-oxidative stress and autophagy activation.
J Asian Nat Prod Res, 26 (5): 583-603. [PMID:37735930]
5. Tung CW, Chan SC, Cheng PH, Chen YC, Wu PM, Lin WC, Chen RJ, Huang BM, Yang SH. (2025)
Exploring Cordycepin as a Neuroprotective Agent in Huntington's Disease: In Vitro and In Vivo Insights.
Pharmacol Res Perspect, 13 (2): e70091. [PMID:40202221]
6. Zhang Z, Tudi T, Liu Y, Zhou S, Feng N, Yang Y, Tang C, Tang Q, Zhang J. (2016)
Preparative isolation of cordycepin, N(6)-(2-hydroxyethyl)-adenosine and adenosine from Cordyceps militaris by macroporous resin and purification by recycling high-speed counter-current chromatography.
J Chromatogr B Analyt Technol Biomed Life Sci, 1033-1034: 218-225. [PMID:27567378]