MiMeDB: Showing metabocard for Cordycepin (MMDBc0015661)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-05-15 06:27:29 UTC

Update Date

2022-08-31 06:39:38 UTC

Metabolite ID

MMDBc0015661

Metabolite Identification

Common Name

Cordycepin

Description

Cordycepin, also known as 3'-deoxyadenosine, belongs to the class of organic compounds known as purine 3'-deoxyribonucleosides. Purine 3'-deoxyribonucleosides are compounds consisting of a purine linked to a ribose which lacks a hydroxyl group at position 3. Cordycepin has displayed cytotoxicity against some leukemic cell lines in vitro, and at least one clinical trial of cordycepin as a leukemia treatment is in progress. Because cordycepin is similar to adenosine, some enzymes cannot discriminate between the two. Cordycepin is a strong basic compound (based on its pKa). Cordycepin has been found to produce rapid, robust imipramine-like antidepressant effects in animal models of depression, and these effects, similarly to those of imipramine, are dependent on enhancement of AMPA receptor signaling. Cordycepin, or 3'-deoxyadenosine, is a derivative of the nucleoside adenosine, differing from the latter by the absence of the hydroxy group in the 3' position of its ribose moiety. It was initially extracted from the fungus Cordyceps militaris, but can now be produced synthetically. It can therefore participate in certain biochemical reactions (for example, incorporation into an mRNA molecule, resulting in premature termination of protein synthesis).

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 05031421362D          

 21 23  0  0  1  0            999 V2000
    0.0992   -1.0091    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -2.0486    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538    1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838   -1.2640    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0992   -0.1841    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9233    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    2.3479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838    0.0709    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.6378    3.1729    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    1.9354    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.6979    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    2.1904    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    0.8555    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9457   -2.2201    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5683    0.3009    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3687   -0.5966    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3004   -1.8474    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6359   -0.5586    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3004    0.6542    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  5  1  1  0  0  0  0
  5  2  1  6  0  0  0
  6  1  1  0  0  0  0
  8  7  2  0  0  0  0
  9  7  1  0  0  0  0
 10  6  1  0  0  0  0
 11  8  1  0  0  0  0
 12  3  2  0  0  0  0
 12  8  1  0  0  0  0
 13  3  1  0  0  0  0
 13  9  2  0  0  0  0
 14  4  2  0  0  0  0
 14  7  1  0  0  0  0
 15  4  1  0  0  0  0
 15  9  1  0  0  0  0
 10 15  1  6  0  0  0
 16  2  1  0  0  0  0
  6 17  1  1  0  0  0
 18  5  1  0  0  0  0
 18 10  1  0  0  0  0
  5 19  1  1  0  0  0
  6 20  1  6  0  0  0
 10 21  1  1  0  0  0
M  END
> <DATABASE_ID>
MMDBc0015661

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@@]1(CO)C[C@@]([H])(O)[C@@]([H])(O1)N1C=NC2=C(N)N=CN=C12

> <INCHI_IDENTIFIER>
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

> <FORMULA>
C10H13N5O3

> <MOLECULAR_WEIGHT>
251.2419

> <EXACT_MASS>
251.101839307

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_AVERAGE_POLARIZABILITY>
24.14563025412037

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3R,5S)-2-(6-amino-9H-purin-9-yl)-5-(hydroxymethyl)oxolan-3-ol

> <ALOGPS_LOGP>
-0.85

> <JCHEM_LOGP>
-1.4006691906666668

> <ALOGPS_LOGS>
-1.35

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.706912091159193

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.52749509396719

> <JCHEM_PKA_STRONGEST_BASIC>
4.988857701284418

> <JCHEM_POLAR_SURFACE_AREA>
119.31000000000002

> <JCHEM_REFRACTIVITY>
62.0985

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.13e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
cordycepin

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 03-MAY-14   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-MAY-14         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   12  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   13  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   14  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   15  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   16  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   19  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   20  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   21  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
CONECT    1    5    6                                                       
CONECT    2    5   16                                                       
CONECT    3   12   13                                                       
CONECT    4   14   15                                                       
CONECT    5    1    2   18   19                                             
CONECT    6    1   10   17   20                                             
CONECT    7    8    9   14                                                  
CONECT    8    7   11   12                                                  
CONECT    9    7   13   15                                                  
CONECT   10    6   15   18   21                                             
CONECT   11    8                                                            
CONECT   12    3    8                                                       
CONECT   13    3    9                                                       
CONECT   14    4    7                                                       
CONECT   15    4    9   10                                                  
CONECT   16    2                                                            
CONECT   17    6                                                            
CONECT   18    5   10                                                       
CONECT   19    5                                                            
CONECT   20    6                                                            
CONECT   21   10                                                            
MASTER        0    0    0    0    0    0    0    0   21    0   46    0
END

Synonyms

Value	Source
9-(beta-D-3'-Deoxyribofuranosyl)adenine	ChEBI
9-Cordyceposidoadenine	ChEBI
Cordycepine	ChEBI
3'-Deoxyadenosine	Kegg
9-(b-D-3'-Deoxyribofuranosyl)adenine	Generator
9-(Β-D-3'-deoxyribofuranosyl)adenine	Generator

Molecular Formula

C₁₀H₁₃N₅O₃

Average Mass

251.2419

Monoisotopic Mass

251.101839307

IUPAC Name

(2R,3R,5S)-2-(6-amino-9H-purin-9-yl)-5-(hydroxymethyl)oxolan-3-ol

Traditional Name

cordycepin

CAS Registry Number

Not Available

SMILES

[H][C@@]1(CO)C[C@@]([H])(O)[C@@]([H])(O1)N1C=NC2=C(N)N=CN=C12

InChI Identifier

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

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as purine 3'-deoxyribonucleosides. Purine 3'-deoxyribonucleosides are compounds consisting of a purine linked to a ribose which lacks a hydroxyl group at position 3.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Purine nucleosides

Sub Class

Purine 3'-deoxyribonucleosides

Direct Parent

Purine 3'-deoxyribonucleosides

Alternative Parents

Substituents

Purine 3'-deoxyribonucleoside
6-aminopurine
Imidazopyrimidine
Purine
Aminopyrimidine
N-substituted imidazole
Pyrimidine
Imidolactam
Azole
Imidazole
Heteroaromatic compound
Tetrahydrofuran
Secondary alcohol
Oxacycle
Azacycle
Organoheterocyclic compound
Amine
Primary amine
Primary alcohol
Organooxygen compound
Organonitrogen compound
Hydrocarbon derivative
Organopnictogen compound
Alcohol
Organic nitrogen compound
Organic oxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

adenosines (CHEBI:29014 )
3'-deoxyribonucleoside (CHEBI:29014 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	11.3 g/L	ALOGPS
logP	-0.85	ALOGPS
logP	-1.4	ChemAxon
logS	-1.4	ALOGPS
pKa (Strongest Acidic)	13.53	ChemAxon
pKa (Strongest Basic)	4.99	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	119.31 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	62.1 m³·mol⁻¹	ChemAxon
Polarizability	24.15 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0a7l-9540000000-15762da69c32bc742914	2017-08-28	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-000i-0940000000-2c067314ffeafb798143	2017-07-25	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-000i-0900000000-7fc851de1b34dfe23c7b	2017-07-25	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-000i-2900000000-bf18fa84d79f0172e854	2017-07-25	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0ue9-0590000000-d6d9e041d5e56ca8ba8a	2017-07-26	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-001i-0910000000-22fd0372519621d4f307	2017-07-26	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-053r-3900000000-f821a579bd26d18f2fa3	2017-07-26	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-18	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Not Available

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
nah	1		Metabolic reconstruction
Eukaryota/Fungi	Ascomycota	3	Human feces	Metabolic reconstruction

Exposure Sources

Source Type	Source Sub-type	Species	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

External Links

HMDB ID

Not Available

DrugBank ID

DB12156

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

C00001495

Chemspider ID

Not Available

KEGG Compound ID

C08431

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Cordycepin

METLIN ID

Not Available

PubChem Compound

6303

PDB ID

Not Available

ChEBI ID

29014

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

van Santen JA, Poynton EF, Iskakova D, McMann E, Alsup TA, Clark TN, Fergusson CH, Fewer DP, Hughes AH, McCadden CA, Parra J, Soldatou S, Rudolf JD, Janssen EM, Duncan KR, Linington RG: The Natural Products Atlas 2.0: a database of microbially-derived natural products. Nucleic Acids Res. 2022 Jan 7;50(D1):D1317-D1323. doi: 10.1093/nar/gkab941. [PubMed:34718710 ]

Showing metabocard for Cordycepin (MMDBc0015661)

MOL for #<Metabolite:0x00007f4697b2c930>

3D MOL for #<Metabolite:0x00007f4697b2c930>

3D SDF for #<Metabolite:0x00007f4697b2c930>

3D-SDF for #<Metabolite:0x00007f4697b2c930>

PDB for #<Metabolite:0x00007f4697b2c930>

3D PDB for #<Metabolite:0x00007f4697b2c930>

SMILES for #<Metabolite:0x00007f4697b2c930>

INCHI for #<Metabolite:0x00007f4697b2c930>

Structure for #<Metabolite:0x00007f4697b2c930>

3D Structure for #<Metabolite:0x00007f4697b2c930>