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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/)
Bioactivity Comments
Modest neuroprotective effects have been reported in in vitro and in vivo Huntington's disease (HD) models, although this did not translate to significant improvement in motor behaviours in the R6/2 HD transgenic mouse model [5]. Activation of autophagy and anti-oxidative stress pathways, and neuroprotective effects have also been reported [2-4].
Transporters Moving this Compound Across a Lipid Membrane
Transporter EC number Reaction Reference
Equilibrative nucleoside transporter 3 1