GtoPdb is requesting financial support from commercial users. Please see our sustainability page for more information.

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].

cordycepin 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 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
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 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/)

For advanced searching click here to open chemical structure editor

Similar Ligands Click here for help
SS148
Click here for ligand page
Targets
CoV Non-structural protein 14; CoV Non-structural protein 16
CoV nsp16 inhibitor 2a [PMID: 34257831]
Click here for ligand page
Targets
CoV Non-structural protein 14; CoV Non-structural protein 16
NSC620333
Click here for ligand page
Targets
CoV Non-structural protein 14
sinefungin
Click here for ligand page
Targets
CoV 2'-O-methyltransferase; CoV Non-structural protein 16
TO507
Click here for ligand page
Targets
CoV Non-structural protein 14
compound 6c [PMID: 34435786]
Click here for ligand page
Targets
A3 receptor
LLY-283
Click here for ligand page
Targets
protein arginine methyltransferase 5
bromo-deaza-SAH
Click here for ligand page
Targets
DNA methyltransferase 1; DOT1 like histone lysine methyltransferase
clofarabine
Click here for ligand page
Targets
ribonucleotide reductase catalytic subunit M1; ribonucleotide reductase regulatory subunit M2
5-Cl-5-deoxy-(±)-ENBA
Click here for ligand page
Targets
A1 receptor
triciribine
Click here for ligand page
[3H]HEMADO
Click here for ligand page
Targets
A3 receptor
HEMADO
Click here for ligand page
Targets
A1 receptor; A2A receptor; A2B receptor; A3 receptor
regadenoson
Click here for ligand page
Targets
A1 receptor; A2A receptor; A2B receptor; A3 receptor
binodenoson
Click here for ligand page
Targets
A1 receptor; A2A receptor; A2B receptor; A3 receptor
GS9667
Click here for ligand page
Targets
A1 receptor; A2A receptor; A2B receptor; A3 receptor
tecadenoson
Click here for ligand page
Targets
A1 receptor; A2A receptor
2'-Me-CCPA
Click here for ligand page
Targets
A3 receptor
TCPA
Click here for ligand page
Targets
A1 receptor; A2A receptor; A2B receptor; A3 receptor
S-adenosylhomocysteine
Click here for ligand page
Targets
S-Adenosylhomocysteine hydrolase
DRB
Click here for ligand page
Targets
Casein kinase 2
AMA
Click here for ligand page
Targets
Histidine decarboxylase
S-adenosyl-L-methioninamine
Click here for ligand page
3-deazaadenosine
Click here for ligand page
Targets
S-Adenosylhomocysteine hydrolase
2'-deoxyadenosine
Click here for ligand page
Targets
Adenosine deaminase
2',5'-dideoxyadenosine
Click here for ligand page
vidarabine
Click here for ligand page
Targets
Equilibrative nucleoside transporter 1; Equilibrative nucleoside transporter 2; Sodium/nucleoside cotransporter 2
fludarabine
Click here for ligand page
Targets
Equilibrative nucleoside transporter 3; Sodium/nucleoside cotransporter 2; ribonucleotide reductase catalytic subunit M1; ribonucleotide reductase regulatory subunit M2
cladribine
Click here for ligand page
Targets
Equilibrative nucleoside transporter 1; Equilibrative nucleoside transporter 2; Equilibrative nucleoside transporter 3; Sodium/nucleoside cotransporter 2; Solute carrier family 28 member 3
S-adenosyl methionine
Click here for ligand page
Targets
S-Adenosylmethionine carrier; S-Adenosylmethionine decarboxylase
tubercidin
Click here for ligand page
Targets
Equilibrative nucleoside transporter 1; Equilibrative nucleoside transporter 2; Equilibrative nucleoside transporter 3
nitrobenzylmercaptopurine ribonucleoside
Click here for ligand page
Targets
Equilibrative nucleoside transporter 1
[3H]nitrobenzylmercaptopurine ribonucleoside
Click here for ligand page
Targets
Equilibrative nucleoside transporter 1
GR79236
Click here for ligand page
Targets
A1 receptor; A2A receptor
adenosine
Click here for ligand page
Targets
A1 receptor; A2A receptor; A2B receptor; A3 receptor; Adenosine deaminase; Adenosine kinase; Equilibrative nucleoside transporter 1; Equilibrative nucleoside transporter 2; Equilibrative nucleoside transporter 3; Plasma membrane monoamine transporter; Sodium/nucleoside cotransporter 2; Solute carrier family 28 member 3; TRPM4; phosphatidylinositol 4-kinase type 2 alpha; phosphatidylinositol 4-kinase type 2 beta... click on ligand to see complete list
[125I]APNEA
Click here for ligand page
Targets
A3 receptor
I-ABA
Click here for ligand page
Targets
A3 receptor
AB-NECA
Click here for ligand page
Targets
A2B receptor
metrifudil
Click here for ligand page
Targets
A2A receptor
N(6)-cyclohexyladenosine
Click here for ligand page
Targets
A1 receptor; A2A receptor; A2B receptor; A3 receptor
CV-1808
Click here for ligand page
Targets
A2A receptor
CV-1674
Click here for ligand page
Targets
A2A receptor
CGS 24012
Click here for ligand page
Targets
A2A receptor
APNEA
Click here for ligand page
Targets
A2A receptor
(S)-PIA
Click here for ligand page
Targets
A1 receptor; A2A receptor; A2B receptor; A3 receptor
(R)-PIA
Click here for ligand page
Targets
A1 receptor; A2A receptor; A2B receptor; A3 receptor
cyclopentyladenosine
Click here for ligand page
Targets
A1 receptor; A2A receptor; A2B receptor; A3 receptor
[3H]CCPA
Click here for ligand page
Targets
A1 receptor
CCPA
Click here for ligand page
Targets
A1 receptor; A2A receptor; A2B receptor; A3 receptor
2-chloroadenosine
Click here for ligand page
Targets
A1 receptor; A2A receptor; A2B receptor; A3 receptor; Equilibrative nucleoside transporter 1; Equilibrative nucleoside transporter 2