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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-11 07:27:50 UTC

Update Date

2021-09-26 23:01:55 UTC

HMDB ID

HMDB0250451

Secondary Accession Numbers

None

Metabolite Identification

Common Name

Cordycepin

Description

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. Based on a literature review a significant number of articles have been published on 3-Deoxyadenosine. This compound has been identified in human blood as reported by (PMID: 31557052 ). Cordycepin is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Cordycepin is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

HMDB0250451
     RDKit          3D
Cordycepin
 31 33  0  0  0  0  0  0  0  0999 V2000
    5.3102    0.6279    0.2512 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.1247    0.5009   -0.4991 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1104    0.6096   -1.8343 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.9562    0.4836   -2.5364 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7980    0.2446   -1.8861 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7567    0.1271   -0.5508 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9350    0.2573    0.1465 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6653    0.1069    1.4383 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3300   -0.1142    1.5334 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7518   -0.1077    0.3433 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6055   -0.2924   -0.0426 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4223    0.7809    0.1905 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7221    0.3675    0.2562 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5875    0.9197   -0.8563 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8888    0.4072   -0.6526 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7405   -1.1415    0.2850 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2946   -1.4219    0.7208 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2617   -1.2149    2.0895 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2102    0.9789   -0.1546 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3377    0.3727    1.2577 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0144    0.5823   -3.6119 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8407   -0.2711    2.4811 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6864   -0.5918   -1.1272 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2032    0.7056    1.2158 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1911    0.5846   -1.8445 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5963    2.0202   -0.7588 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0632    0.2737    0.3168 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9006   -1.5782   -0.7137 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4318   -1.5384    1.0478 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9495   -2.4043    0.4071 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5960   -0.2750    2.2375 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  0
 13 24  1  0
 14 25  1  0
 14 26  1  0
 15 27  1  0
 16 28  1  0
 16 29  1  0
 17 30  1  0
 18 31  1  0
M  END


  Mrv1533004241515212D          

 18 20  0  0  0  0            999 V2000
    3.2789    2.0625    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.2789    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934    0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2789   -0.4125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.5645    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5645    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7798    1.0799    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2949    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7798   -0.2549    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.5249   -1.0396    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0098   -1.7070    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5249   -2.3744    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7798   -3.1591    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5868   -3.3306    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7403   -2.1195    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7403   -1.2945    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0728   -0.8096    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  2  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
  6 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
 11 17  1  0  0  0  0
 17 18  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0250451

> <DATABASE_NAME>
hmdb

> <SMILES>
NC1=C2N=CN(C3OC(CO)CC3O)C2=NC=N1

> <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)

> <INCHI_KEY>
OFEZSBMBBKLLBJ-UHFFFAOYSA-N

> <FORMULA>
C10H13N5O3

> <MOLECULAR_WEIGHT>
251.246

> <EXACT_MASS>
251.101839299

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
31

> <JCHEM_AVERAGE_POLARIZABILITY>
24.226460305103863

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
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>
13.527495093967161

> <JCHEM_PKA_STRONGEST_BASIC>
4.98884814804849

> <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>
3deoxyadenosine

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0250451
     RDKit          3D
Cordycepin
 31 33  0  0  0  0  0  0  0  0999 V2000
    5.3102    0.6279    0.2512 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.1247    0.5009   -0.4991 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1104    0.6096   -1.8343 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.9562    0.4836   -2.5364 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7980    0.2446   -1.8861 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7567    0.1271   -0.5508 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9350    0.2573    0.1465 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6653    0.1069    1.4383 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3300   -0.1142    1.5334 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7518   -0.1077    0.3433 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6055   -0.2924   -0.0426 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4223    0.7809    0.1905 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7221    0.3675    0.2562 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5875    0.9197   -0.8563 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8888    0.4072   -0.6526 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7405   -1.1415    0.2850 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2946   -1.4219    0.7208 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2617   -1.2149    2.0895 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2102    0.9789   -0.1546 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3377    0.3727    1.2577 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0144    0.5823   -3.6119 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8407   -0.2711    2.4811 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6864   -0.5918   -1.1272 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2032    0.7056    1.2158 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1911    0.5846   -1.8445 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5963    2.0202   -0.7588 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0632    0.2737    0.3168 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9006   -1.5782   -0.7137 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4318   -1.5384    1.0478 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9495   -2.4043    0.4071 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5960   -0.2750    2.2375 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  0
 13 24  1  0
 14 25  1  0
 14 26  1  0
 15 27  1  0
 16 28  1  0
 16 29  1  0
 17 30  1  0
 18 31  1  0
M  END

HEADER    PROTEIN                                 24-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-APR-15         0                                  
HETATM    1  N   UNK     0       6.121   3.850   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       6.121   2.310   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0       7.454   1.540   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0       7.454   0.000   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0       6.121  -0.770   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0       4.787   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.787   1.540   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0       3.322   2.016   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0       2.417   0.770   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0       3.322  -0.476   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0       2.846  -1.941   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       3.752  -3.186   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       2.846  -4.432   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       3.322  -5.897   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       4.829  -6.217   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       1.382  -3.956   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       1.382  -2.416   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       0.136  -1.511   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    7                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7   10                                                  
CONECT    7    6    2    8                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9    6   11                                                  
CONECT   11   10   12   17                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14   16                                                  
CONECT   14   13   15                                                       
CONECT   15   14                                                            
CONECT   16   13   17                                                       
CONECT   17   16   11   18                                                  
CONECT   18   17                                                            
MASTER        0    0    0    0    0    0    0    0   18    0   40    0
END

COMPND    HMDB0250451
HETATM    1  N1  UNL     1       5.310   0.628   0.251  1.00  0.00           N  
HETATM    2  C1  UNL     1       4.125   0.501  -0.499  1.00  0.00           C  
HETATM    3  N2  UNL     1       4.110   0.610  -1.834  1.00  0.00           N  
HETATM    4  C2  UNL     1       2.956   0.484  -2.536  1.00  0.00           C  
HETATM    5  N3  UNL     1       1.798   0.245  -1.886  1.00  0.00           N  
HETATM    6  C3  UNL     1       1.757   0.127  -0.551  1.00  0.00           C  
HETATM    7  C4  UNL     1       2.935   0.257   0.146  1.00  0.00           C  
HETATM    8  N4  UNL     1       2.665   0.107   1.438  1.00  0.00           N  
HETATM    9  C5  UNL     1       1.330  -0.114   1.533  1.00  0.00           C  
HETATM   10  N5  UNL     1       0.752  -0.108   0.343  1.00  0.00           N  
HETATM   11  C6  UNL     1      -0.605  -0.292  -0.043  1.00  0.00           C  
HETATM   12  O1  UNL     1      -1.422   0.781   0.190  1.00  0.00           O  
HETATM   13  C7  UNL     1      -2.722   0.367   0.256  1.00  0.00           C  
HETATM   14  C8  UNL     1      -3.588   0.920  -0.856  1.00  0.00           C  
HETATM   15  O2  UNL     1      -4.889   0.407  -0.653  1.00  0.00           O  
HETATM   16  C9  UNL     1      -2.741  -1.141   0.285  1.00  0.00           C  
HETATM   17  C10 UNL     1      -1.295  -1.422   0.721  1.00  0.00           C  
HETATM   18  O3  UNL     1      -1.262  -1.215   2.089  1.00  0.00           O  
HETATM   19  H1  UNL     1       6.210   0.979  -0.155  1.00  0.00           H  
HETATM   20  H2  UNL     1       5.338   0.373   1.258  1.00  0.00           H  
HETATM   21  H3  UNL     1       3.014   0.582  -3.612  1.00  0.00           H  
HETATM   22  H4  UNL     1       0.841  -0.271   2.481  1.00  0.00           H  
HETATM   23  H5  UNL     1      -0.686  -0.592  -1.127  1.00  0.00           H  
HETATM   24  H6  UNL     1      -3.203   0.706   1.216  1.00  0.00           H  
HETATM   25  H7  UNL     1      -3.191   0.585  -1.844  1.00  0.00           H  
HETATM   26  H8  UNL     1      -3.596   2.020  -0.759  1.00  0.00           H  
HETATM   27  H9  UNL     1      -5.063   0.274   0.317  1.00  0.00           H  
HETATM   28  H10 UNL     1      -2.901  -1.578  -0.714  1.00  0.00           H  
HETATM   29  H11 UNL     1      -3.432  -1.538   1.048  1.00  0.00           H  
HETATM   30  H12 UNL     1      -0.950  -2.404   0.407  1.00  0.00           H  
HETATM   31  H13 UNL     1      -1.596  -0.275   2.237  1.00  0.00           H  
CONECT    1    2   19   20
CONECT    2    3    3    7
CONECT    3    4
CONECT    4    5    5   21
CONECT    5    6
CONECT    6    7    7   10
CONECT    7    8
CONECT    8    9    9
CONECT    9   10   22
CONECT   10   11
CONECT   11   12   17   23
CONECT   12   13
CONECT   13   14   16   24
CONECT   14   15   25   26
CONECT   15   27
CONECT   16   17   28   29
CONECT   17   18   30
CONECT   18   31
END

HMDB0250451
     RDKit          3D
Cordycepin
 31 33  0  0  0  0  0  0  0  0999 V2000
    5.3102    0.6279    0.2512 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.1247    0.5009   -0.4991 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1104    0.6096   -1.8343 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.9562    0.4836   -2.5364 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7980    0.2446   -1.8861 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7567    0.1271   -0.5508 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9350    0.2573    0.1465 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6653    0.1069    1.4383 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3300   -0.1142    1.5334 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7518   -0.1077    0.3433 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6055   -0.2924   -0.0426 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4223    0.7809    0.1905 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7221    0.3675    0.2562 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5875    0.9197   -0.8563 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8888    0.4072   -0.6526 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7405   -1.1415    0.2850 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2946   -1.4219    0.7208 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2617   -1.2149    2.0895 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2102    0.9789   -0.1546 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3377    0.3727    1.2577 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0144    0.5823   -3.6119 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8407   -0.2711    2.4811 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6864   -0.5918   -1.1272 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2032    0.7056    1.2158 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1911    0.5846   -1.8445 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5963    2.0202   -0.7588 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0632    0.2737    0.3168 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9006   -1.5782   -0.7137 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4318   -1.5384    1.0478 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9495   -2.4043    0.4071 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5960   -0.2750    2.2375 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  0
 13 24  1  0
 14 25  1  0
 14 26  1  0
 15 27  1  0
 16 28  1  0
 16 29  1  0
 17 30  1  0
 18 31  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Not Available

Chemical Formula

C₁₀H₁₃N₅O₃

Average Molecular Weight

251.246

Monoisotopic Molecular Weight

251.101839299

IUPAC Name

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

Traditional Name

3deoxyadenosine

CAS Registry Number

Not Available

SMILES

NC1=C2N=CN(C3OC(CO)CC3O)C2=NC=N1

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)

InChI Key

OFEZSBMBBKLLBJ-UHFFFAOYSA-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

a small molecule (CPD-10129 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 31557052)

Process

Not Available

Role

Not Available

Physical Properties

State

Not Available

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular 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)	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	24.23 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

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DeepCCS	[M+H]+	156.776	30932474
DeepCCS	[M-H]-	154.418	30932474
DeepCCS	[M-2H]-	187.567	30932474
DeepCCS	[M+Na]+	162.869	30932474
AllCCS	[M+H]+	157.7	32859911
AllCCS	[M+H-H2O]+	153.9	32859911
AllCCS	[M+NH4]+	161.2	32859911
AllCCS	[M+Na]+	162.2	32859911
AllCCS	[M-H]-	157.0	32859911
AllCCS	[M+Na-2H]-	156.6	32859911
AllCCS	[M+HCOO]-	156.3	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Cordycepin	NC1=C2N=CN(C3OC(CO)CC3O)C2=NC=N1	3174.1	Standard polar	33892256
Cordycepin	NC1=C2N=CN(C3OC(CO)CC3O)C2=NC=N1	2032.0	Standard non polar	33892256
Cordycepin	NC1=C2N=CN(C3OC(CO)CC3O)C2=NC=N1	2498.6	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Cordycepin,3TMS,isomer #1	C[Si](C)(C)NC1=NC=NC2=C1N=CN2C1OC(CO[Si](C)(C)C)CC1O[Si](C)(C)C	2544.3	Semi standard non polar	33892256
Cordycepin,3TMS,isomer #1	C[Si](C)(C)NC1=NC=NC2=C1N=CN2C1OC(CO[Si](C)(C)C)CC1O[Si](C)(C)C	2560.6	Standard non polar	33892256
Cordycepin,3TMS,isomer #1	C[Si](C)(C)NC1=NC=NC2=C1N=CN2C1OC(CO[Si](C)(C)C)CC1O[Si](C)(C)C	3722.5	Standard polar	33892256
Cordycepin,3TMS,isomer #2	C[Si](C)(C)OCC1CC(O)C(N2C=NC3=C(N([Si](C)(C)C)[Si](C)(C)C)N=CN=C32)O1	2560.0	Semi standard non polar	33892256
Cordycepin,3TMS,isomer #2	C[Si](C)(C)OCC1CC(O)C(N2C=NC3=C(N([Si](C)(C)C)[Si](C)(C)C)N=CN=C32)O1	2749.0	Standard non polar	33892256
Cordycepin,3TMS,isomer #2	C[Si](C)(C)OCC1CC(O)C(N2C=NC3=C(N([Si](C)(C)C)[Si](C)(C)C)N=CN=C32)O1	3564.9	Standard polar	33892256
Cordycepin,3TMS,isomer #3	C[Si](C)(C)OC1CC(CO)OC1N1C=NC2=C(N([Si](C)(C)C)[Si](C)(C)C)N=CN=C21	2549.6	Semi standard non polar	33892256
Cordycepin,3TMS,isomer #3	C[Si](C)(C)OC1CC(CO)OC1N1C=NC2=C(N([Si](C)(C)C)[Si](C)(C)C)N=CN=C21	2682.6	Standard non polar	33892256
Cordycepin,3TMS,isomer #3	C[Si](C)(C)OC1CC(CO)OC1N1C=NC2=C(N([Si](C)(C)C)[Si](C)(C)C)N=CN=C21	3523.3	Standard polar	33892256
Cordycepin,4TMS,isomer #1	C[Si](C)(C)OCC1CC(O[Si](C)(C)C)C(N2C=NC3=C(N([Si](C)(C)C)[Si](C)(C)C)N=CN=C32)O1	2572.4	Semi standard non polar	33892256
Cordycepin,4TMS,isomer #1	C[Si](C)(C)OCC1CC(O[Si](C)(C)C)C(N2C=NC3=C(N([Si](C)(C)C)[Si](C)(C)C)N=CN=C32)O1	2661.1	Standard non polar	33892256
Cordycepin,4TMS,isomer #1	C[Si](C)(C)OCC1CC(O[Si](C)(C)C)C(N2C=NC3=C(N([Si](C)(C)C)[Si](C)(C)C)N=CN=C32)O1	3178.6	Standard polar	33892256
Cordycepin,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)NC1=NC=NC2=C1N=CN2C1OC(CO[Si](C)(C)C(C)(C)C)CC1O[Si](C)(C)C(C)(C)C	3127.9	Semi standard non polar	33892256
Cordycepin,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)NC1=NC=NC2=C1N=CN2C1OC(CO[Si](C)(C)C(C)(C)C)CC1O[Si](C)(C)C(C)(C)C	3203.6	Standard non polar	33892256
Cordycepin,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)NC1=NC=NC2=C1N=CN2C1OC(CO[Si](C)(C)C(C)(C)C)CC1O[Si](C)(C)C(C)(C)C	3796.6	Standard polar	33892256
Cordycepin,3TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OCC1CC(O)C(N2C=NC3=C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)N=CN=C32)O1	3125.3	Semi standard non polar	33892256
Cordycepin,3TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OCC1CC(O)C(N2C=NC3=C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)N=CN=C32)O1	3371.0	Standard non polar	33892256
Cordycepin,3TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OCC1CC(O)C(N2C=NC3=C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)N=CN=C32)O1	3625.2	Standard polar	33892256
Cordycepin,3TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OC1CC(CO)OC1N1C=NC2=C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)N=CN=C21	3106.8	Semi standard non polar	33892256
Cordycepin,3TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OC1CC(CO)OC1N1C=NC2=C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)N=CN=C21	3301.5	Standard non polar	33892256
Cordycepin,3TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OC1CC(CO)OC1N1C=NC2=C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)N=CN=C21	3588.8	Standard polar	33892256
Cordycepin,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCC1CC(O[Si](C)(C)C(C)(C)C)C(N2C=NC3=C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)N=CN=C32)O1	3268.8	Semi standard non polar	33892256
Cordycepin,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCC1CC(O[Si](C)(C)C(C)(C)C)C(N2C=NC3=C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)N=CN=C32)O1	3461.3	Standard non polar	33892256
Cordycepin,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCC1CC(O[Si](C)(C)C(C)(C)C)C(N2C=NC3=C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)N=CN=C32)O1	3450.6	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Cordycepin GC-MS (Non-derivatized) - 70eV, Positive	splash10-0006-9330000000-36ebcaa2784a4d37eee4	2021-09-23	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Cordycepin GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Cordycepin GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Cordycepin GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Cordycepin GC-MS (TMS_1_3) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Cordycepin GC-MS (TMS_2_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Cordycepin GC-MS (TMS_2_2) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Cordycepin GC-MS (TMS_2_3) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Cordycepin GC-MS (TMS_2_4) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Cordycepin GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Cordycepin GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Cordycepin GC-MS (TBDMS_1_3) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Cordycepin GC-MS (TBDMS_2_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Cordycepin GC-MS (TBDMS_2_2) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Cordycepin GC-MS (TBDMS_2_3) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Cordycepin GC-MS (TBDMS_2_4) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cordycepin 10V, Positive-QTOF	splash10-000i-0920000000-6b3aed5b54305ca4eb67	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cordycepin 20V, Positive-QTOF	splash10-000i-0900000000-c1ee2199364d0258bae1	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cordycepin 40V, Positive-QTOF	splash10-000i-1900000000-09511fabedcbaa7998da	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cordycepin 10V, Negative-QTOF	splash10-0udi-0190000000-1316cc417b36449db30c	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cordycepin 20V, Negative-QTOF	splash10-001i-0900000000-d79b1dec18f268981b4e	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cordycepin 40V, Negative-QTOF	splash10-0a59-0900000000-5530837e9e649331da89	2021-10-12	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	31557052	details

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

217130

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Cordycepin

METLIN ID

Not Available

PubChem Compound

248010

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]

Enzymes

Enzyme Details

1. Equilibrative nucleoside transporter 3

General function:: Involved in nucleoside transmembrane transporter activity
Specific function:: Mediates both influx and efflux of nucleosides across the membrane (equilibrative transporter). Mediates transport of adenine, adenosine and uridine, as well as several nucleoside analog drugs, such as anticancer and antiviral agents, including cladribine, cordycepin, tubercidin and AZT. Does not transport hypoxanthine
Gene Name:: SLC29A3
Uniprot ID:: Q9BZD2
Molecular weight:: 51799.9

Showing metabocard for Cordycepin (HMDB0250451)

MOL for HMDB0250451 (Cordycepin)

3D MOL for HMDB0250451 (Cordycepin)

3D SDF for HMDB0250451 (Cordycepin)

3D-SDF for HMDB0250451 (Cordycepin)

PDB for HMDB0250451 (Cordycepin)

3D PDB for HMDB0250451 (Cordycepin)

SMILES for HMDB0250451 (Cordycepin)

INCHI for HMDB0250451 (Cordycepin)

Structure for HMDB0250451 (Cordycepin)

3D Structure for HMDB0250451 (Cordycepin)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

Enzymes