NP-MRD: Showing NP-Card for Cordycepin (NP0005117)

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Record Information

Version

1.0

Created at

2020-12-09 02:27:36 UTC

Updated at

2021-08-19 23:59:37 UTC

NP-MRD ID

NP0005117

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Cordycepin

Provided By

NPAtlas

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 is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. Cordycepin is found in Cordyceps militaris and Cordyceps sinensis . It was first documented in 1950 (PMID: 14796634). Based on a literature review a significant number of articles have been published on Cordycepin (PMID: 34581939) (PMID: 34575692) (PMID: 34513126) (PMID: 34512317) (PMID: 34488549) (PMID: 34455933).

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306242118173D          

 31 33  0  0  0  0            999 V2000
    5.1380    1.0247    0.7340 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.7974    1.2747    0.3673 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3563    2.5430    0.2948 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0676    2.8058   -0.0569 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1883    1.8315   -0.3436 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.5821    0.5649   -0.2842 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8965    0.2764    0.0736 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0024   -1.0457    0.0497 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.8232   -1.5684   -0.3030 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9367   -0.5795   -0.5121 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4326   -0.8247   -0.9070 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.1729    0.3214   -1.0415 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4896   -0.1685   -0.9366 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.4853    0.9597   -0.8279 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.7482    0.3877   -0.7294 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4058   -0.9219    0.3745 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.0769   -1.6318    0.2185 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.3513   -2.9374   -0.1866 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8210    0.5253    0.0908 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5287    1.3174    1.6562 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7485    3.8341   -0.1049 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6457   -2.6513   -0.3968 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5106   -1.4012   -1.8444 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7295   -0.8947   -1.7270 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4653    1.5925   -1.7190 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2687    1.5059    0.1174 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1765    0.5287    0.1399 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2528   -1.6273    0.5012 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3485   -0.2253    1.2380 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4723   -1.5876    1.1406 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1457   -3.2281    0.3618 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 13 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
  7  2  1  0  0  0  0
 17 11  1  0  0  0  0
 10  6  1  0  0  0  0
  1 19  1  0  0  0  0
  1 20  1  0  0  0  0
  4 21  1  0  0  0  0
  9 22  1  0  0  0  0
 11 23  1  6  0  0  0
 13 24  1  6  0  0  0
 14 25  1  0  0  0  0
 14 26  1  0  0  0  0
 15 27  1  0  0  0  0
 16 28  1  0  0  0  0
 16 29  1  0  0  0  0
 17 30  1  1  0  0  0
 18 31  1  0  0  0  0
M  END

     RDKit          3D

 31 33  0  0  0  0  0  0  0  0999 V2000
    5.1380    1.0247    0.7340 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.7974    1.2747    0.3673 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3563    2.5430    0.2948 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0676    2.8058   -0.0569 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1883    1.8315   -0.3436 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.5821    0.5649   -0.2842 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8965    0.2764    0.0736 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0024   -1.0457    0.0497 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.8232   -1.5684   -0.3030 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9367   -0.5795   -0.5121 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4326   -0.8247   -0.9070 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.1729    0.3214   -1.0415 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4896   -0.1685   -0.9366 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.4853    0.9597   -0.8279 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7482    0.3877   -0.7294 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4058   -0.9219    0.3745 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0769   -1.6318    0.2185 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.3513   -2.9374   -0.1866 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8210    0.5253    0.0908 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5287    1.3174    1.6562 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7485    3.8341   -0.1049 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6457   -2.6513   -0.3968 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5106   -1.4012   -1.8444 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7295   -0.8947   -1.7270 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4653    1.5925   -1.7190 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2687    1.5059    0.1174 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1765    0.5287    0.1399 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2528   -1.6273    0.5012 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3485   -0.2253    1.2380 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4723   -1.5876    1.1406 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1457   -3.2281    0.3618 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 13 16  1  0
 16 17  1  0
 17 18  1  0
  7  2  1  0
 17 11  1  0
 10  6  1  0
  1 19  1  0
  1 20  1  0
  4 21  1  0
  9 22  1  0
 11 23  1  6
 13 24  1  6
 14 25  1  0
 14 26  1  0
 15 27  1  0
 16 28  1  0
 16 29  1  0
 17 30  1  1
 18 31  1  0
M  END


  Mrv1652306242118173D          

 31 33  0  0  0  0            999 V2000
    5.1380    1.0247    0.7340 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.7974    1.2747    0.3673 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3563    2.5430    0.2948 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0676    2.8058   -0.0569 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1883    1.8315   -0.3436 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.5821    0.5649   -0.2842 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8965    0.2764    0.0736 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0024   -1.0457    0.0497 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.8232   -1.5684   -0.3030 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9367   -0.5795   -0.5121 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4326   -0.8247   -0.9070 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.1729    0.3214   -1.0415 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4896   -0.1685   -0.9366 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.4853    0.9597   -0.8279 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.7482    0.3877   -0.7294 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4058   -0.9219    0.3745 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.0769   -1.6318    0.2185 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.3513   -2.9374   -0.1866 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8210    0.5253    0.0908 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5287    1.3174    1.6562 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7485    3.8341   -0.1049 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6457   -2.6513   -0.3968 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5106   -1.4012   -1.8444 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7295   -0.8947   -1.7270 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4653    1.5925   -1.7190 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2687    1.5059    0.1174 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1765    0.5287    0.1399 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2528   -1.6273    0.5012 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3485   -0.2253    1.2380 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4723   -1.5876    1.1406 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1457   -3.2281    0.3618 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 13 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
  7  2  1  0  0  0  0
 17 11  1  0  0  0  0
 10  6  1  0  0  0  0
  1 19  1  0  0  0  0
  1 20  1  0  0  0  0
  4 21  1  0  0  0  0
  9 22  1  0  0  0  0
 11 23  1  6  0  0  0
 13 24  1  6  0  0  0
 14 25  1  0  0  0  0
 14 26  1  0  0  0  0
 15 27  1  0  0  0  0
 16 28  1  0  0  0  0
 16 29  1  0  0  0  0
 17 30  1  1  0  0  0
 18 31  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0005117

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]OC([H])([H])[C@@]1([H])O[C@@]([H])(N2C([H])=NC3=C2N=C([H])N=C3N([H])[H])[C@]([H])(O[H])C1([H])[H]

> <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_ATOM_COUNT>
31

> <JCHEM_AVERAGE_POLARIZABILITY>
24.49778483329087

> <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>
14.706912091083211

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.527495092894476

> <JCHEM_PKA_STRONGEST_BASIC>
3.922164775410645

> <JCHEM_POLAR_SURFACE_AREA>
119.31000000000002

> <JCHEM_REFRACTIVITY>
62.09850000000001

> <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

$$$$

     RDKit          3D

 31 33  0  0  0  0  0  0  0  0999 V2000
    5.1380    1.0247    0.7340 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.7974    1.2747    0.3673 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3563    2.5430    0.2948 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0676    2.8058   -0.0569 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1883    1.8315   -0.3436 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.5821    0.5649   -0.2842 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8965    0.2764    0.0736 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0024   -1.0457    0.0497 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.8232   -1.5684   -0.3030 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9367   -0.5795   -0.5121 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4326   -0.8247   -0.9070 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.1729    0.3214   -1.0415 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4896   -0.1685   -0.9366 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.4853    0.9597   -0.8279 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7482    0.3877   -0.7294 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4058   -0.9219    0.3745 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0769   -1.6318    0.2185 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.3513   -2.9374   -0.1866 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8210    0.5253    0.0908 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5287    1.3174    1.6562 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7485    3.8341   -0.1049 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6457   -2.6513   -0.3968 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5106   -1.4012   -1.8444 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7295   -0.8947   -1.7270 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4653    1.5925   -1.7190 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2687    1.5059    0.1174 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1765    0.5287    0.1399 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2528   -1.6273    0.5012 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3485   -0.2253    1.2380 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4723   -1.5876    1.1406 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1457   -3.2281    0.3618 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 13 16  1  0
 16 17  1  0
 17 18  1  0
  7  2  1  0
 17 11  1  0
 10  6  1  0
  1 19  1  0
  1 20  1  0
  4 21  1  0
  9 22  1  0
 11 23  1  6
 13 24  1  6
 14 25  1  0
 14 26  1  0
 15 27  1  0
 16 28  1  0
 16 29  1  0
 17 30  1  1
 18 31  1  0
M  END

HEADER    PROTEIN                                 24-JUN-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-JUN-21         0                                  
HETATM    1  N   UNK     0       5.138   1.025   0.734  0.00  0.00           N+0
HETATM    2  C   UNK     0       3.797   1.275   0.367  0.00  0.00           C+0
HETATM    3  N   UNK     0       3.356   2.543   0.295  0.00  0.00           N+0
HETATM    4  C   UNK     0       2.068   2.806  -0.057  0.00  0.00           C+0
HETATM    5  N   UNK     0       1.188   1.831  -0.344  0.00  0.00           N+0
HETATM    6  C   UNK     0       1.582   0.565  -0.284  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.897   0.276   0.074  0.00  0.00           C+0
HETATM    8  N   UNK     0       3.002  -1.046   0.050  0.00  0.00           N+0
HETATM    9  C   UNK     0       1.823  -1.568  -0.303  0.00  0.00           C+0
HETATM   10  N   UNK     0       0.937  -0.580  -0.512  0.00  0.00           N+0
HETATM   11  C   UNK     0      -0.433  -0.825  -0.907  0.00  0.00           C+0
HETATM   12  O   UNK     0      -1.173   0.321  -1.042  0.00  0.00           O+0
HETATM   13  C   UNK     0      -2.490  -0.169  -0.937  0.00  0.00           C+0
HETATM   14  C   UNK     0      -3.485   0.960  -0.828  0.00  0.00           C+0
HETATM   15  O   UNK     0      -4.748   0.388  -0.729  0.00  0.00           O+0
HETATM   16  C   UNK     0      -2.406  -0.922   0.375  0.00  0.00           C+0
HETATM   17  C   UNK     0      -1.077  -1.632   0.219  0.00  0.00           C+0
HETATM   18  O   UNK     0      -1.351  -2.937  -0.187  0.00  0.00           O+0
HETATM   19  H   UNK     0       5.821   0.525   0.091  0.00  0.00           H+0
HETATM   20  H   UNK     0       5.529   1.317   1.656  0.00  0.00           H+0
HETATM   21  H   UNK     0       1.749   3.834  -0.105  0.00  0.00           H+0
HETATM   22  H   UNK     0       1.646  -2.651  -0.397  0.00  0.00           H+0
HETATM   23  H   UNK     0      -0.511  -1.401  -1.844  0.00  0.00           H+0
HETATM   24  H   UNK     0      -2.729  -0.895  -1.727  0.00  0.00           H+0
HETATM   25  H   UNK     0      -3.465   1.593  -1.719  0.00  0.00           H+0
HETATM   26  H   UNK     0      -3.269   1.506   0.117  0.00  0.00           H+0
HETATM   27  H   UNK     0      -5.176   0.529   0.140  0.00  0.00           H+0
HETATM   28  H   UNK     0      -3.253  -1.627   0.501  0.00  0.00           H+0
HETATM   29  H   UNK     0      -2.349  -0.225   1.238  0.00  0.00           H+0
HETATM   30  H   UNK     0      -0.472  -1.588   1.141  0.00  0.00           H+0
HETATM   31  H   UNK     0      -2.146  -3.228   0.362  0.00  0.00           H+0
CONECT    1    2   19   20                                                  
CONECT    2    1    3    7                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   21                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7   10                                                  
CONECT    7    6    8    2                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10   22                                                  
CONECT   10    9   11    6                                                  
CONECT   11   10   12   17   23                                             
CONECT   12   11   13                                                       
CONECT   13   12   14   16   24                                             
CONECT   14   13   15   25   26                                             
CONECT   15   14   27                                                       
CONECT   16   13   17   28   29                                             
CONECT   17   16   18   11   30                                             
CONECT   18   17   31                                                       
CONECT   19    1                                                            
CONECT   20    1                                                            
CONECT   21    4                                                            
CONECT   22    9                                                            
CONECT   23   11                                                            
CONECT   24   13                                                            
CONECT   25   14                                                            
CONECT   26   14                                                            
CONECT   27   15                                                            
CONECT   28   16                                                            
CONECT   29   16                                                            
CONECT   30   17                                                            
CONECT   31   18                                                            
MASTER        0    0    0    0    0    0    0    0   31    0   66    0
END

RDKit          3D

31 33  0  0  0  0  0  0  0  0999 V2000
    5.1380    1.0247    0.7340 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.7974    1.2747    0.3673 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3563    2.5430    0.2948 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0676    2.8058   -0.0569 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1883    1.8315   -0.3436 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.5821    0.5649   -0.2842 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8965    0.2764    0.0736 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0024   -1.0457    0.0497 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.8232   -1.5684   -0.3030 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9367   -0.5795   -0.5121 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4326   -0.8247   -0.9070 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.1729    0.3214   -1.0415 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4896   -0.1685   -0.9366 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.4853    0.9597   -0.8279 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7482    0.3877   -0.7294 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4058   -0.9219    0.3745 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0769   -1.6318    0.2185 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.3513   -2.9374   -0.1866 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8210    0.5253    0.0908 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5287    1.3174    1.6562 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7485    3.8341   -0.1049 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6457   -2.6513   -0.3968 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5106   -1.4012   -1.8444 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7295   -0.8947   -1.7270 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4653    1.5925   -1.7190 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2687    1.5059    0.1174 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1765    0.5287    0.1399 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2528   -1.6273    0.5012 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3485   -0.2253    1.2380 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4723   -1.5876    1.1406 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1457   -3.2281    0.3618 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 13 16  1  0
 16 17  1  0
 17 18  1  0
  7  2  1  0
 17 11  1  0
 10  6  1  0
  1 19  1  0
  1 20  1  0
  4 21  1  0
  9 22  1  0
 11 23  1  6
 13 24  1  6
 14 25  1  0
 14 26  1  0
 15 27  1  0
 16 28  1  0
 16 29  1  0
 17 30  1  1
 18 31  1  0
M  END

View in JSmol View NMR Assignments

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
Cordycepene	MeSH

Chemical Formula

C₁₀H₁₃N₅O₃

Average Mass

251.2419 Da

Monoisotopic Mass

251.10184 Da

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

NC1=NC=NC2=C1N=CN2[C@@H]1O[C@H](CO)C[C@H]1O

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

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Allium cepa	KNApSAcK Database	22123792
Cordyceps militaris	NPAtlas	14796634
Ophiocordyceps sinensis	Fungi	KNApSAcK

Species Where Detected

Species Name	Source	Reference
Aspergillus nidulans	KNApSAcK Database	22123792
Cordyceps sinensis	KNApSAcK Database	22123792

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 )

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	495.00 to 496.00 °C. @ 760.00 mm Hg	The Good Scents Company Information System
Water Solubility	6.9e-07 mg/L @ 25 °C (est)	The Good Scents Company Information System
LogP	11.680	The Good Scents Company Information System

Predicted Properties

Property	Value	Source
logP	-0.85	ALOGPS
logP	-1.4	ChemAxon
logS	-1.4	ALOGPS
pKa (Strongest Acidic)	13.53	ChemAxon
pKa (Strongest Basic)	3.92	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	24.5 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

External Links

NPAtlas ID

NPA015446

HMDB ID

Not Available

DrugBank ID

DB12156

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00001495

Chemspider ID

6064

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

Good Scents ID

rw1429691

References

General References

CUNNINGHAM KG, MANSON W, SPRING FS, HUTCHINSON SA: Cordycepin, a metabolic product isolated from cultures of Cordyceps militaris (Linn.) Link. Nature. 1950 Dec 2;166(4231):949. doi: 10.1038/166949a0. [PubMed:14796634 ]
Sun X, Tan Y, Lyu J, Liu HL, Zhao ZM, Liu CH: Active Components Formulation Developed from Fuzheng Huayu Recipe () for Anti-Liver Fibrosis. Chin J Integr Med. 2021 Sep 28. pii: 10.1007/s11655-021-3293-x. doi: 10.1007/s11655-021-3293-x. [PubMed:34581939 ]
Patil S, Reda R, Boreak N, Taher HA, Melha AA, Albrakati A, Vinothkumar TS, Mustafa M, Robaian A, Alroomy R, Kharaf RJA, Kameli TS, Alkahtani A, Baeshen HA, Patil VR, Testarelli L: Adipogenic Stimulation and Pyrrolidine Dithiocarbamate Induced Osteogenic Inhibition of Dental Pulp Stem Cells Is Countered by Cordycepin. J Pers Med. 2021 Sep 14;11(9). pii: jpm11090915. doi: 10.3390/jpm11090915. [PubMed:34575692 ]
Chen J, Li HF, Zhao G, Lin JM, He X: Matrix-assisted laser desorption ionization mass spectrometry based quantitative analysis of cordycepin from Cordyceps militaris. J Pharm Anal. 2021 Aug;11(4):499-504. doi: 10.1016/j.jpha.2021.05.003. Epub 2021 Jul 2. [PubMed:34513126 ]
Mishra J, Khan W, Ahmad S, Misra K: Supercritical Carbon Dioxide Extracts of Cordyceps sinensis: Chromatography-based Metabolite Profiling and Protective Efficacy Against Hypobaric Hypoxia. Front Pharmacol. 2021 Aug 26;12:628924. doi: 10.3389/fphar.2021.628924. eCollection 2021. [PubMed:34512317 ]
Ku CW, Ho TJ, Huang CY, Chu PM, Ou HC, Hsieh PL: Cordycepin Attenuates Palmitic Acid-Induced Inflammation and Apoptosis of Vascular Endothelial Cells through Mediating PI3K/Akt/eNOS Signaling Pathway. Am J Chin Med. 2021 Sep 7:1-20. doi: 10.1142/S0192415X21500804. [PubMed:34488549 ]
Nandi R, Bhowmik D, Srivastava R, Prakash A, Kumar D: Discovering potential inhibitors against SARS-CoV-2 by targeting Nsp13 Helicase. J Biomol Struct Dyn. 2021 Aug 28:1-13. doi: 10.1080/07391102.2021.1970024. [PubMed:34455933 ]
Zuo SQ, Li C, Liu YL, Tan YH, Wan X, Xu T, Li Q, Wang L, Wu YL, Deng FM, Tang B: Cordycepin inhibits cell senescence by ameliorating lysosomal dysfunction and inducing autophagy through the AMPK and mTOR-p70S6K pathway. FEBS Open Bio. 2021 Oct;11(10):2705-2714. doi: 10.1002/2211-5463.13263. Epub 2021 Aug 27. [PubMed:34448542 ]
Chen YY, Chen CH, Lin WC, Tung CW, Chen YC, Yang SH, Huang BM, Chen RJ: The Role of Autophagy in Anti-Cancer and Health Promoting Effects of Cordycepin. Molecules. 2021 Aug 16;26(16). pii: molecules26164954. doi: 10.3390/molecules26164954. [PubMed:34443541 ]

Showing NP-Card for Cordycepin (NP0005117)

MOL for NP0005117 (Cordycepin)

3D MOL for NP0005117 (Cordycepin)

3D SDF for NP0005117 (Cordycepin)

3D-SDF for NP0005117 (Cordycepin)

PDB for NP0005117 (Cordycepin)

3D PDB for NP0005117 (Cordycepin)

SMILES for NP0005117 (Cordycepin)

INCHI for NP0005117 (Cordycepin)

Structure for NP0005117 (Cordycepin)

3D Structure for NP0005117 (Cordycepin)