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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-10 22:36:58 UTC

Update Date

2021-09-26 22:54:05 UTC

HMDB ID

HMDB0245554

Secondary Accession Numbers

None

Metabolite Identification

Common Name

2',5'-Dideoxyadenosine

Description

2',5'-Dideoxyadenosine belongs to the class of organic compounds known as 2',5'-dideoxyribonucleosides. These are nucleosides characterized by a purine or pyrimidine base, which is N-linked to a 2',5'-dideoxyribose moiety. Based on a literature review a significant number of articles have been published on 2',5'-Dideoxyadenosine. This compound has been identified in human blood as reported by (PMID: 31557052 ). 2',5'-dideoxyadenosine is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 2',5'-Dideoxyadenosine 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

HMDB0245554
     RDKit          3D
2',5'-Dideoxyadenosine
 30 32  0  0  0  0  0  0  0  0999 V2000
   -3.9602    0.8783   -0.6971 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5735    0.9363   -0.0947 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6000    0.8543   -1.0493 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8084   -0.2305   -0.8239 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4899    0.2152   -0.3484 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7182    1.3561    0.3239 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0372    1.3830    0.5710 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6409    0.3096    0.0826 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9505   -0.0929    0.0901 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9177    0.7266    0.7145 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.2487   -1.2567   -0.5021 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.2827   -1.9998   -1.0839 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9955   -1.6011   -1.0896 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6475   -0.4492   -0.5127 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4375   -1.0871    0.2340 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3410   -0.1005    0.9466 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4849   -0.6865    1.4350 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4914   -0.0694   -0.4481 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5895    1.7429   -0.4070 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8434    0.9348   -1.8056 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4933    1.9418    0.3997 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6429   -0.8262   -1.7254 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0165    2.0975    0.6053 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2034    1.6210    0.2752 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3530    0.4532    1.6097 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5766   -2.9495   -1.5582 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0321   -1.8884   -0.2446 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6814   -1.4732    0.9337 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7727    0.3072    1.8320 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2932   -1.0467    2.3371 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
  9 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  2  0
  4 15  1  0
 15 16  1  0
 16 17  1  0
 16  2  1  0
 14  5  1  0
 14  8  1  0
  1 18  1  0
  1 19  1  0
  1 20  1  0
  2 21  1  0
  4 22  1  0
  6 23  1  0
 10 24  1  0
 10 25  1  0
 12 26  1  0
 15 27  1  0
 15 28  1  0
 16 29  1  0
 17 30  1  0
M  END


  Mrv1652309112100372D          

 17 19  0  0  0  0            999 V2000
   -1.8505    2.3190    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1831    1.8341    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3984    2.0890    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0865    1.4216    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3984    0.7541    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1831    1.0091    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435   -0.0305    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6284   -0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435   -1.3654    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6411   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6411   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556    0.1271    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0701   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0701   -1.1104    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556   -1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556   -2.3479    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435    2.8736    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  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  2  6  1  0  0  0  0
  5  7  1  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  2  0  0  0  0
  7 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
 14 15  2  0  0  0  0
 10 15  1  0  0  0  0
 15 16  1  0  0  0  0
  3 17  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0245554

> <DATABASE_NAME>
hmdb

> <SMILES>
CC1OC(CC1O)N1C=NC2=C1N=CN=C2N

> <INCHI_IDENTIFIER>
InChI=1S/C10H13N5O2/c1-5-6(16)2-7(17-5)15-4-14-8-9(11)12-3-13-10(8)15/h3-7,16H,2H2,1H3,(H2,11,12,13)

> <INCHI_KEY>
FFHPXOJTVQDVMO-UHFFFAOYSA-N

> <FORMULA>
C10H13N5O2

> <MOLECULAR_WEIGHT>
235.247

> <EXACT_MASS>
235.106924679

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
30

> <JCHEM_AVERAGE_POLARIZABILITY>
23.619709199155018

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
5-(6-amino-9H-purin-9-yl)-2-methyloxolan-3-ol

> <ALOGPS_LOGP>
-0.37

> <JCHEM_LOGP>
-0.14341584200000024

> <ALOGPS_LOGS>
-1.55

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
18.54023110616825

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.065468501402847

> <JCHEM_PKA_STRONGEST_BASIC>
3.940920020582946

> <JCHEM_POLAR_SURFACE_AREA>
99.08

> <JCHEM_REFRACTIVITY>
60.14119999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.67e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-(6-aminopurin-9-yl)-2-methyloxolan-3-ol

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0245554
     RDKit          3D
2',5'-Dideoxyadenosine
 30 32  0  0  0  0  0  0  0  0999 V2000
   -3.9602    0.8783   -0.6971 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5735    0.9363   -0.0947 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6000    0.8543   -1.0493 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8084   -0.2305   -0.8239 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4899    0.2152   -0.3484 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7182    1.3561    0.3239 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0372    1.3830    0.5710 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6409    0.3096    0.0826 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9505   -0.0929    0.0901 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9177    0.7266    0.7145 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.2487   -1.2567   -0.5021 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.2827   -1.9998   -1.0839 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9955   -1.6011   -1.0896 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6475   -0.4492   -0.5127 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4375   -1.0871    0.2340 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3410   -0.1005    0.9466 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4849   -0.6865    1.4350 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4914   -0.0694   -0.4481 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5895    1.7429   -0.4070 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8434    0.9348   -1.8056 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4933    1.9418    0.3997 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6429   -0.8262   -1.7254 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0165    2.0975    0.6053 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2034    1.6210    0.2752 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3530    0.4532    1.6097 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5766   -2.9495   -1.5582 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0321   -1.8884   -0.2446 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6814   -1.4732    0.9337 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7727    0.3072    1.8320 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2932   -1.0467    2.3371 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
  9 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  2  0
  4 15  1  0
 15 16  1  0
 16 17  1  0
 16  2  1  0
 14  5  1  0
 14  8  1  0
  1 18  1  0
  1 19  1  0
  1 20  1  0
  2 21  1  0
  4 22  1  0
  6 23  1  0
 10 24  1  0
 10 25  1  0
 12 26  1  0
 15 27  1  0
 15 28  1  0
 16 29  1  0
 17 30  1  0
M  END

HEADER    PROTEIN                                 11-SEP-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-21         0                                  
HETATM    1  C   UNK     0      -3.454   4.329   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -2.208   3.424   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.744   3.899   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.161   2.654   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.744   1.408   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -2.208   1.884   0.000  0.00  0.00           O+0
HETATM    7  N   UNK     0      -0.268  -0.057   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0      -1.173  -1.303   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0      -0.268  -2.549   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0       1.197  -2.073   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.197  -0.533   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0       2.530   0.237   0.000  0.00  0.00           N+0
HETATM   13  C   UNK     0       3.864  -0.533   0.000  0.00  0.00           C+0
HETATM   14  N   UNK     0       3.864  -2.073   0.000  0.00  0.00           N+0
HETATM   15  C   UNK     0       2.530  -2.843   0.000  0.00  0.00           C+0
HETATM   16  N   UNK     0       2.530  -4.383   0.000  0.00  0.00           N+0
HETATM   17  O   UNK     0      -0.268   5.364   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    6                                                  
CONECT    3    2    4   17                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5    2                                                       
CONECT    7    5    8   11                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11   15                                                  
CONECT   11   10    7   12                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   10   16                                                  
CONECT   16   15                                                            
CONECT   17    3                                                            
MASTER        0    0    0    0    0    0    0    0   17    0   38    0
END

COMPND    HMDB0245554
HETATM    1  C1  UNL     1      -3.960   0.878  -0.697  1.00  0.00           C  
HETATM    2  C2  UNL     1      -2.573   0.936  -0.095  1.00  0.00           C  
HETATM    3  O1  UNL     1      -1.600   0.854  -1.049  1.00  0.00           O  
HETATM    4  C3  UNL     1      -0.808  -0.231  -0.824  1.00  0.00           C  
HETATM    5  N1  UNL     1       0.490   0.215  -0.348  1.00  0.00           N  
HETATM    6  C4  UNL     1       0.718   1.356   0.324  1.00  0.00           C  
HETATM    7  N2  UNL     1       2.037   1.383   0.571  1.00  0.00           N  
HETATM    8  C5  UNL     1       2.641   0.310   0.083  1.00  0.00           C  
HETATM    9  C6  UNL     1       3.951  -0.093   0.090  1.00  0.00           C  
HETATM   10  N3  UNL     1       4.918   0.727   0.714  1.00  0.00           N  
HETATM   11  N4  UNL     1       4.249  -1.257  -0.502  1.00  0.00           N  
HETATM   12  C7  UNL     1       3.283  -2.000  -1.084  1.00  0.00           C  
HETATM   13  N5  UNL     1       1.996  -1.601  -1.090  1.00  0.00           N  
HETATM   14  C8  UNL     1       1.648  -0.449  -0.513  1.00  0.00           C  
HETATM   15  C9  UNL     1      -1.438  -1.087   0.234  1.00  0.00           C  
HETATM   16  C10 UNL     1      -2.341  -0.100   0.947  1.00  0.00           C  
HETATM   17  O2  UNL     1      -3.485  -0.687   1.435  1.00  0.00           O  
HETATM   18  H1  UNL     1      -4.491  -0.069  -0.448  1.00  0.00           H  
HETATM   19  H2  UNL     1      -4.589   1.743  -0.407  1.00  0.00           H  
HETATM   20  H3  UNL     1      -3.843   0.935  -1.806  1.00  0.00           H  
HETATM   21  H4  UNL     1      -2.493   1.942   0.400  1.00  0.00           H  
HETATM   22  H5  UNL     1      -0.643  -0.826  -1.725  1.00  0.00           H  
HETATM   23  H6  UNL     1      -0.017   2.098   0.605  1.00  0.00           H  
HETATM   24  H7  UNL     1       5.203   1.621   0.275  1.00  0.00           H  
HETATM   25  H8  UNL     1       5.353   0.453   1.610  1.00  0.00           H  
HETATM   26  H9  UNL     1       3.577  -2.949  -1.558  1.00  0.00           H  
HETATM   27  H10 UNL     1      -2.032  -1.888  -0.245  1.00  0.00           H  
HETATM   28  H11 UNL     1      -0.681  -1.473   0.934  1.00  0.00           H  
HETATM   29  H12 UNL     1      -1.773   0.307   1.832  1.00  0.00           H  
HETATM   30  H13 UNL     1      -3.293  -1.047   2.337  1.00  0.00           H  
CONECT    1    2   18   19   20
CONECT    2    3   16   21
CONECT    3    4
CONECT    4    5   15   22
CONECT    5    6   14
CONECT    6    7    7   23
CONECT    7    8
CONECT    8    9    9   14
CONECT    9   10   11
CONECT   10   24   25
CONECT   11   12   12
CONECT   12   13   26
CONECT   13   14   14
CONECT   15   16   27   28
CONECT   16   17   29
CONECT   17   30
END

HMDB0245554
     RDKit          3D
2',5'-Dideoxyadenosine
 30 32  0  0  0  0  0  0  0  0999 V2000
   -3.9602    0.8783   -0.6971 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5735    0.9363   -0.0947 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6000    0.8543   -1.0493 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8084   -0.2305   -0.8239 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4899    0.2152   -0.3484 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7182    1.3561    0.3239 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0372    1.3830    0.5710 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6409    0.3096    0.0826 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9505   -0.0929    0.0901 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9177    0.7266    0.7145 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.2487   -1.2567   -0.5021 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.2827   -1.9998   -1.0839 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9955   -1.6011   -1.0896 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6475   -0.4492   -0.5127 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4375   -1.0871    0.2340 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3410   -0.1005    0.9466 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4849   -0.6865    1.4350 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4914   -0.0694   -0.4481 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5895    1.7429   -0.4070 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8434    0.9348   -1.8056 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4933    1.9418    0.3997 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6429   -0.8262   -1.7254 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0165    2.0975    0.6053 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2034    1.6210    0.2752 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3530    0.4532    1.6097 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5766   -2.9495   -1.5582 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0321   -1.8884   -0.2446 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6814   -1.4732    0.9337 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7727    0.3072    1.8320 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2932   -1.0467    2.3371 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
  9 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  2  0
  4 15  1  0
 15 16  1  0
 16 17  1  0
 16  2  1  0
 14  5  1  0
 14  8  1  0
  1 18  1  0
  1 19  1  0
  1 20  1  0
  2 21  1  0
  4 22  1  0
  6 23  1  0
 10 24  1  0
 10 25  1  0
 12 26  1  0
 15 27  1  0
 15 28  1  0
 16 29  1  0
 17 30  1  0
M  END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Not Available

Chemical Formula

C₁₀H₁₃N₅O₂

Average Molecular Weight

235.247

Monoisotopic Molecular Weight

235.106924679

IUPAC Name

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

Traditional Name

5-(6-aminopurin-9-yl)-2-methyloxolan-3-ol

CAS Registry Number

Not Available

SMILES

CC1OC(CC1O)N1C=NC2=C1N=CN=C2N

InChI Identifier

InChI=1S/C10H13N5O2/c1-5-6(16)2-7(17-5)15-4-14-8-9(11)12-3-13-10(8)15/h3-7,16H,2H2,1H3,(H2,11,12,13)

InChI Key

FFHPXOJTVQDVMO-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 2',5'-dideoxyribonucleosides. These are nucleosides characterized by a purine or pyrimidine base, which is N-linked to a 2',5'-dideoxyribose moiety.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

2',5'-dideoxyribonucleosides

Sub Class

Not Available

Direct Parent

2',5'-dideoxyribonucleosides

Alternative Parents

Substituents

2',5'-dideoxyribonucleoside
6-aminopurine
Imidazopyrimidine
Purine
Aminopyrimidine
N-substituted imidazole
Pyrimidine
Imidolactam
Azole
Imidazole
Heteroaromatic compound
Tetrahydrofuran
Secondary alcohol
Oxacycle
Azacycle
Organoheterocyclic compound
Amine
Primary amine
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

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 31557052)

Source

Exogenous

Exogenous (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	-0.37	ALOGPS
logP	-0.14	ChemAxon
logS	-1.6	ALOGPS
pKa (Strongest Acidic)	14.07	ChemAxon
pKa (Strongest Basic)	3.94	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	99.08 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	60.14 m³·mol⁻¹	ChemAxon
Polarizability	23.62 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	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]+	146.995	30932474
DeepCCS	[M-H]-	144.637	30932474
DeepCCS	[M-2H]-	178.571	30932474
DeepCCS	[M+Na]+	154.216	30932474
AllCCS	[M+H]+	154.5	32859911
AllCCS	[M+H-H2O]+	150.5	32859911
AllCCS	[M+NH4]+	158.1	32859911
AllCCS	[M+Na]+	159.1	32859911
AllCCS	[M-H]-	154.4	32859911
AllCCS	[M+Na-2H]-	154.1	32859911
AllCCS	[M+HCOO]-	153.9	32859911

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Predicted by Siyang on May 30, 2022	9.6136 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	2.55 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	1637.7 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	265.5 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	96.9 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	164.0 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	81.0 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	313.6 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	323.0 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	115.1 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	663.5 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	256.0 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	836.7 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	184.4 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	244.3 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	333.1 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	238.0 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	39.2 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
2',5'-Dideoxyadenosine	CC1OC(CC1O)N1C=NC2=C1N=CN=C2N	2981.4	Standard polar	33892256
2',5'-Dideoxyadenosine	CC1OC(CC1O)N1C=NC2=C1N=CN=C2N	2284.9	Standard non polar	33892256
2',5'-Dideoxyadenosine	CC1OC(CC1O)N1C=NC2=C1N=CN=C2N	2266.5	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
2',5'-Dideoxyadenosine,2TMS,isomer #1	CC1OC(N2C=NC3=C(N[Si](C)(C)C)N=CN=C32)CC1O[Si](C)(C)C	2344.7	Semi standard non polar	33892256
2',5'-Dideoxyadenosine,2TMS,isomer #1	CC1OC(N2C=NC3=C(N[Si](C)(C)C)N=CN=C32)CC1O[Si](C)(C)C	2336.2	Standard non polar	33892256
2',5'-Dideoxyadenosine,2TMS,isomer #1	CC1OC(N2C=NC3=C(N[Si](C)(C)C)N=CN=C32)CC1O[Si](C)(C)C	3420.3	Standard polar	33892256
2',5'-Dideoxyadenosine,2TMS,isomer #2	CC1OC(N2C=NC3=C(N([Si](C)(C)C)[Si](C)(C)C)N=CN=C32)CC1O	2346.7	Semi standard non polar	33892256
2',5'-Dideoxyadenosine,2TMS,isomer #2	CC1OC(N2C=NC3=C(N([Si](C)(C)C)[Si](C)(C)C)N=CN=C32)CC1O	2536.4	Standard non polar	33892256
2',5'-Dideoxyadenosine,2TMS,isomer #2	CC1OC(N2C=NC3=C(N([Si](C)(C)C)[Si](C)(C)C)N=CN=C32)CC1O	3425.9	Standard polar	33892256
2',5'-Dideoxyadenosine,3TMS,isomer #1	CC1OC(N2C=NC3=C(N([Si](C)(C)C)[Si](C)(C)C)N=CN=C32)CC1O[Si](C)(C)C	2375.2	Semi standard non polar	33892256
2',5'-Dideoxyadenosine,3TMS,isomer #1	CC1OC(N2C=NC3=C(N([Si](C)(C)C)[Si](C)(C)C)N=CN=C32)CC1O[Si](C)(C)C	2498.6	Standard non polar	33892256
2',5'-Dideoxyadenosine,3TMS,isomer #1	CC1OC(N2C=NC3=C(N([Si](C)(C)C)[Si](C)(C)C)N=CN=C32)CC1O[Si](C)(C)C	2991.2	Standard polar	33892256
2',5'-Dideoxyadenosine,2TBDMS,isomer #1	CC1OC(N2C=NC3=C(N[Si](C)(C)C(C)(C)C)N=CN=C32)CC1O[Si](C)(C)C(C)(C)C	2722.2	Semi standard non polar	33892256
2',5'-Dideoxyadenosine,2TBDMS,isomer #1	CC1OC(N2C=NC3=C(N[Si](C)(C)C(C)(C)C)N=CN=C32)CC1O[Si](C)(C)C(C)(C)C	2838.8	Standard non polar	33892256
2',5'-Dideoxyadenosine,2TBDMS,isomer #1	CC1OC(N2C=NC3=C(N[Si](C)(C)C(C)(C)C)N=CN=C32)CC1O[Si](C)(C)C(C)(C)C	3525.4	Standard polar	33892256
2',5'-Dideoxyadenosine,2TBDMS,isomer #2	CC1OC(N2C=NC3=C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)N=CN=C32)CC1O	2717.6	Semi standard non polar	33892256
2',5'-Dideoxyadenosine,2TBDMS,isomer #2	CC1OC(N2C=NC3=C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)N=CN=C32)CC1O	3007.0	Standard non polar	33892256
2',5'-Dideoxyadenosine,2TBDMS,isomer #2	CC1OC(N2C=NC3=C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)N=CN=C32)CC1O	3467.4	Standard polar	33892256
2',5'-Dideoxyadenosine,3TBDMS,isomer #1	CC1OC(N2C=NC3=C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)N=CN=C32)CC1O[Si](C)(C)C(C)(C)C	2899.2	Semi standard non polar	33892256
2',5'-Dideoxyadenosine,3TBDMS,isomer #1	CC1OC(N2C=NC3=C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)N=CN=C32)CC1O[Si](C)(C)C(C)(C)C	3183.0	Standard non polar	33892256
2',5'-Dideoxyadenosine,3TBDMS,isomer #1	CC1OC(N2C=NC3=C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)N=CN=C32)CC1O[Si](C)(C)C(C)(C)C	3205.2	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - 2',5'-Dideoxyadenosine GC-MS (Non-derivatized) - 70eV, Positive	splash10-054o-8930000000-3e150155f949feef9bdf	2021-09-23	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2',5'-Dideoxyadenosine GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2',5'-Dideoxyadenosine GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2',5'-Dideoxyadenosine GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2',5'-Dideoxyadenosine GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2',5'-Dideoxyadenosine GC-MS (TBDMS_1_2) - 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 - 2',5'-Dideoxyadenosine 10V, Positive-QTOF	splash10-000i-0900000000-c1ee2199364d0258bae1	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2',5'-Dideoxyadenosine 20V, Positive-QTOF	splash10-000i-0900000000-c1ee2199364d0258bae1	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2',5'-Dideoxyadenosine 40V, Positive-QTOF	splash10-0670-1900000000-30275b60919aeb1d28a0	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2',5'-Dideoxyadenosine 10V, Negative-QTOF	splash10-001i-0190000000-431845e941718e11d753	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2',5'-Dideoxyadenosine 20V, Negative-QTOF	splash10-001i-0900000000-acd39155280d96b4614a	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2',5'-Dideoxyadenosine 40V, Negative-QTOF	splash10-0a59-1900000000-ccdb7151bff538d7ceff	2021-10-12	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	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

2936

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

3044

PDB ID

Not Available

ChEBI ID

93820

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 ]

Showing metabocard for 2',5'-Dideoxyadenosine (HMDB0245554)

MOL for HMDB0245554 (2',5'-Dideoxyadenosine)

3D MOL for HMDB0245554 (2',5'-Dideoxyadenosine)

3D SDF for HMDB0245554 (2',5'-Dideoxyadenosine)

3D-SDF for HMDB0245554 (2',5'-Dideoxyadenosine)

PDB for HMDB0245554 (2',5'-Dideoxyadenosine)

3D PDB for HMDB0245554 (2',5'-Dideoxyadenosine)

SMILES for HMDB0245554 (2',5'-Dideoxyadenosine)

INCHI for HMDB0245554 (2',5'-Dideoxyadenosine)

Structure for HMDB0245554 (2',5'-Dideoxyadenosine)

3D Structure for HMDB0245554 (2',5'-Dideoxyadenosine)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra