MiMeDB: Showing metabocard for Deoxyadenosine (MMDBc0000334)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2020-12-10 18:28:57 UTC

Update Date

2024-10-17 19:00:08 UTC

Metabolite ID

MMDBc0000334

Metabolite Identification

Common Name

Deoxyadenosine

Description

Deoxyadenosine is a derivative of the nucleoside adenosine. It is composed of adenine attached to a deoxyribose moiety via a N9-glycosidic bond. Deoxyribose differs from ribose by the absence of oxygen in the 3' position of its ribose ring. Deoxyadenosine is a critical component of DNA. When present in sufficiently high levels, deoxyadensoine can act as an immunotoxin and a metabotoxin. An immunotoxin disrupts, limits the function, or destroys immune cells. A metabotoxin is an endogenous metabolite that causes adverse health effects at chronically high levels. Chronically high levels of deoxyadenosine are associated with adenosine deaminase (ADA) deficiency, an inborn error of metabolism. ADA deficiency damages the immune system and causes severe combined immunodeficiency (SCID). People with SCID lack virtually all immune protection from bacteria, viruses, and fungi. They are prone to repeated and persistent infections that can be very serious or life-threatening. These infections are often caused by "opportunistic" organisms that ordinarily do not cause illness in people with a normal immune system. The main symptoms of ADA deficiency are pneumonia, chronic diarrhea, and widespread skin rashes. The mechanism by which dATP functions as an immunotoxin is as follows: because deoxyadenosine is a precursor to dATP, a buildup of dATP in cells inhibits ribonucleotide reductase and prevents DNA synthesis, so cells are unable to divide. Since developing T cells and B cells are some of the most mitotically active cells, they are unable to divide and propagate to respond to immune challenges. High levels of deoxyadenosine also lead to an increase in S-adenosylhomocysteine, which is toxic to immature lymphocytes.

Structure

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

HMDB0000101
     RDKit          3D
Deoxyadenosine
 31 33  0  0  0  0  0  0  0  0999 V2000
    5.3171    0.1584   -0.4503 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.0540   -0.4307   -0.2195 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9340   -1.6502    0.3103 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.7238   -2.1955    0.5231 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5830   -1.5504    0.2179 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6392   -0.3268   -0.3149 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8766    0.2338   -0.5339 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6498    1.4285   -1.0597 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3316    1.6110   -1.1665 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6760    0.5064   -0.6983 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7412    0.4108   -0.6852 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.3075   -0.9513   -0.7384 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4458   -0.8687    0.2898 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.5591   -1.5521   -0.1301 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6405    0.6326    0.3348 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.4527    1.0589    1.5336 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4593    2.4480    1.6386 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3134    1.0675    0.4293 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.4403    0.9953   -1.0458 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1663   -0.2551   -0.0103 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7237   -3.1957    0.9596 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8892    2.5110   -1.5681 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1423    0.9734   -1.5700 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8376   -1.1654   -1.7129 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6491   -1.7875   -0.5504 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0565   -1.1987    1.2740 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0506   -1.9621    0.6474 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0628    0.9669   -0.6133 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1249    0.5619    2.4616 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5090    0.7630    1.3213 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6525    2.7627    2.1272 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
 13 15  1  0
 15 16  1  0
 16 17  1  0
 15 18  1  0
  7  2  1  0
 18 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
 12 24  1  0
 12 25  1  0
 13 26  1  1
 14 27  1  0
 15 28  1  6
 16 29  1  0
 16 30  1  0
 17 31  1  0
M  END


  Mrv1652309032023522D          

 18 20  0  0  1  0            999 V2000
    0.9372   -0.2267    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.9372   -1.0517    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2227   -1.4642    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.2226   -2.2892    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9371   -2.7017    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6516   -2.2892    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6516   -1.4642    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4362   -1.2093    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.9211   -1.8768    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4362   -2.5442    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6911   -3.3290    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.2062   -3.9963    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6911   -4.6639    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.4361   -5.4485    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9882   -6.0616    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4757   -4.4089    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.1432   -4.8939    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4758   -3.5839    0.0000 C   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
  2  7  2  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
  6 10  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
 11 10  1  1  0  0  0
 11 12  1  0  0  0  0
 11 18  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  1  0  0  0
 13 16  1  0  0  0  0
 14 15  1  0  0  0  0
 16 17  1  6  0  0  0
 16 18  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0000334

> <DATABASE_NAME>
MIME

> <SMILES>
NC1=C2N=CN([C@H]3C[C@H](O)[C@@H](CO)O3)C2=NC=N1

> <INCHI_IDENTIFIER>
InChI=1S/C10H13N5O3/c11-9-8-10(13-3-12-9)15(4-14-8)7-1-5(17)6(2-16)18-7/h3-7,16-17H,1-2H2,(H2,11,12,13)/t5-,6+,7+/m0/s1

> <INCHI_KEY>
OLXZPDWKRNYJJZ-RRKCRQDMSA-N

> <FORMULA>
C10H13N5O3

> <MOLECULAR_WEIGHT>
251.2419

> <EXACT_MASS>
251.101839307

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
31

> <JCHEM_AVERAGE_POLARIZABILITY>
24.236037685868787

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-0.95

> <JCHEM_LOGP>
-1.1903258086666668

> <ALOGPS_LOGS>
-1.37

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.785037392135134

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.886733808608756

> <JCHEM_PKA_STRONGEST_BASIC>
3.9409008296129784

> <JCHEM_POLAR_SURFACE_AREA>
119.30999999999999

> <JCHEM_REFRACTIVITY>
61.68489999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.07e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-deoxyadenosine

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0000101
     RDKit          3D
Deoxyadenosine
 31 33  0  0  0  0  0  0  0  0999 V2000
    5.3171    0.1584   -0.4503 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.0540   -0.4307   -0.2195 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9340   -1.6502    0.3103 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.7238   -2.1955    0.5231 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5830   -1.5504    0.2179 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6392   -0.3268   -0.3149 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8766    0.2338   -0.5339 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6498    1.4285   -1.0597 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3316    1.6110   -1.1665 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6760    0.5064   -0.6983 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7412    0.4108   -0.6852 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.3075   -0.9513   -0.7384 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4458   -0.8687    0.2898 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.5591   -1.5521   -0.1301 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6405    0.6326    0.3348 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.4527    1.0589    1.5336 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4593    2.4480    1.6386 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3134    1.0675    0.4293 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.4403    0.9953   -1.0458 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1663   -0.2551   -0.0103 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7237   -3.1957    0.9596 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8892    2.5110   -1.5681 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1423    0.9734   -1.5700 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8376   -1.1654   -1.7129 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6491   -1.7875   -0.5504 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0565   -1.1987    1.2740 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0506   -1.9621    0.6474 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0628    0.9669   -0.6133 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1249    0.5619    2.4616 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5090    0.7630    1.3213 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6525    2.7627    2.1272 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
 13 15  1  0
 15 16  1  0
 16 17  1  0
 15 18  1  0
  7  2  1  0
 18 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
 12 24  1  0
 12 25  1  0
 13 26  1  1
 14 27  1  0
 15 28  1  6
 16 29  1  0
 16 30  1  0
 17 31  1  0
M  END

HEADER    PROTEIN                                 03-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-SEP-20         0                                  
HETATM    1  N   UNK     0       1.749  -0.423   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       1.749  -1.963   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0       0.416  -2.733   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0       0.416  -4.273   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0       1.749  -5.043   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0       3.083  -4.273   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.083  -2.733   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0       4.548  -2.257   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0       5.453  -3.503   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0       4.548  -4.749   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0       5.023  -6.214   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       4.118  -7.460   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       5.023  -8.706   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.547 -10.171   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       5.578 -11.315   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       6.488  -8.230   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       7.734  -9.135   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       6.488  -6.690   0.000  0.00  0.00           C+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    2    6    8                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    6    9   11                                                  
CONECT   11   10   12   18                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14   16                                                  
CONECT   14   13   15                                                       
CONECT   15   14                                                            
CONECT   16   13   17   18                                                  
CONECT   17   16                                                            
CONECT   18   11   16                                                       
MASTER        0    0    0    0    0    0    0    0   18    0   40    0
END

COMPND    HMDB0000101
HETATM    1  N1  UNL     1       5.317   0.158  -0.450  1.00  0.00           N  
HETATM    2  C1  UNL     1       4.054  -0.431  -0.219  1.00  0.00           C  
HETATM    3  N2  UNL     1       3.934  -1.650   0.310  1.00  0.00           N  
HETATM    4  C2  UNL     1       2.724  -2.196   0.523  1.00  0.00           C  
HETATM    5  N3  UNL     1       1.583  -1.550   0.218  1.00  0.00           N  
HETATM    6  C3  UNL     1       1.639  -0.327  -0.315  1.00  0.00           C  
HETATM    7  C4  UNL     1       2.877   0.234  -0.534  1.00  0.00           C  
HETATM    8  N4  UNL     1       2.650   1.429  -1.060  1.00  0.00           N  
HETATM    9  C5  UNL     1       1.332   1.611  -1.166  1.00  0.00           C  
HETATM   10  N5  UNL     1       0.676   0.506  -0.698  1.00  0.00           N  
HETATM   11  C6  UNL     1      -0.741   0.411  -0.685  1.00  0.00           C  
HETATM   12  C7  UNL     1      -1.308  -0.951  -0.738  1.00  0.00           C  
HETATM   13  C8  UNL     1      -2.446  -0.869   0.290  1.00  0.00           C  
HETATM   14  O1  UNL     1      -3.559  -1.552  -0.130  1.00  0.00           O  
HETATM   15  C9  UNL     1      -2.640   0.633   0.335  1.00  0.00           C  
HETATM   16  C10 UNL     1      -3.453   1.059   1.534  1.00  0.00           C  
HETATM   17  O2  UNL     1      -3.459   2.448   1.639  1.00  0.00           O  
HETATM   18  O3  UNL     1      -1.313   1.068   0.429  1.00  0.00           O  
HETATM   19  H1  UNL     1       5.440   0.995  -1.046  1.00  0.00           H  
HETATM   20  H2  UNL     1       6.166  -0.255  -0.010  1.00  0.00           H  
HETATM   21  H3  UNL     1       2.724  -3.196   0.960  1.00  0.00           H  
HETATM   22  H4  UNL     1       0.889   2.511  -1.568  1.00  0.00           H  
HETATM   23  H5  UNL     1      -1.142   0.973  -1.570  1.00  0.00           H  
HETATM   24  H6  UNL     1      -1.838  -1.165  -1.713  1.00  0.00           H  
HETATM   25  H7  UNL     1      -0.649  -1.787  -0.550  1.00  0.00           H  
HETATM   26  H8  UNL     1      -2.056  -1.199   1.274  1.00  0.00           H  
HETATM   27  H9  UNL     1      -4.051  -1.962   0.647  1.00  0.00           H  
HETATM   28  H10 UNL     1      -3.063   0.967  -0.613  1.00  0.00           H  
HETATM   29  H11 UNL     1      -3.125   0.562   2.462  1.00  0.00           H  
HETATM   30  H12 UNL     1      -4.509   0.763   1.321  1.00  0.00           H  
HETATM   31  H13 UNL     1      -2.653   2.763   2.127  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   18   23
CONECT   12   13   24   25
CONECT   13   14   15   26
CONECT   14   27
CONECT   15   16   18   28
CONECT   16   17   29   30
CONECT   17   31
END

HMDB0000101
     RDKit          3D
Deoxyadenosine
 31 33  0  0  0  0  0  0  0  0999 V2000
    5.3171    0.1584   -0.4503 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.0540   -0.4307   -0.2195 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9340   -1.6502    0.3103 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.7238   -2.1955    0.5231 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5830   -1.5504    0.2179 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6392   -0.3268   -0.3149 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8766    0.2338   -0.5339 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6498    1.4285   -1.0597 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3316    1.6110   -1.1665 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6760    0.5064   -0.6983 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7412    0.4108   -0.6852 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.3075   -0.9513   -0.7384 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4458   -0.8687    0.2898 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.5591   -1.5521   -0.1301 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6405    0.6326    0.3348 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.4527    1.0589    1.5336 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4593    2.4480    1.6386 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3134    1.0675    0.4293 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.4403    0.9953   -1.0458 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1663   -0.2551   -0.0103 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7237   -3.1957    0.9596 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8892    2.5110   -1.5681 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1423    0.9734   -1.5700 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8376   -1.1654   -1.7129 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6491   -1.7875   -0.5504 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0565   -1.1987    1.2740 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0506   -1.9621    0.6474 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0628    0.9669   -0.6133 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1249    0.5619    2.4616 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5090    0.7630    1.3213 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6525    2.7627    2.1272 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
 13 15  1  0
 15 16  1  0
 16 17  1  0
 15 18  1  0
  7  2  1  0
 18 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
 12 24  1  0
 12 25  1  0
 13 26  1  1
 14 27  1  0
 15 28  1  6
 16 29  1  0
 16 30  1  0
 17 31  1  0
M  END

Synonyms

Value	Source
(2R,3S,5R)-5-(6-Amino-9H-purin-9-yl)-2-(hydroxymethyl)tetrahydrofuran-3-ol	ChEBI
5-(6-AMINO-purin-9-yl)-2-hydroxymethyl-tetrahydro-furan-3-ol	ChEBI
9-(2-Deoxy-beta-D-erythro-pentofuranosyl)adenine	ChEBI
9-(2-Deoxy-beta-D-ribofuranosyl)-9H-purin-6-amine	ChEBI
Adenine deoxyribonucleoside	ChEBI
Adenyldeoxyriboside	ChEBI
dA	ChEBI
2'-Deoxyadenosine	Kegg
9-(2-Deoxy-b-D-erythro-pentofuranosyl)adenine	Generator
9-(2-Deoxy-β-D-erythro-pentofuranosyl)adenine	Generator
9-(2-Deoxy-b-D-ribofuranosyl)-9H-purin-6-amine	Generator
9-(2-Deoxy-β-D-ribofuranosyl)-9H-purin-6-amine	Generator
1-(6-Amino-9H-purin-9-yl)-1,2-dideoxy-b-D-ribofuranose	HMDB
1-(6-Amino-9H-purin-9-yl)-1,2-dideoxy-beta-D-ribofuranose	HMDB
1-(6-Amino-9H-purin-9-yl)-1,2-dideoxy-beta-delta-ribofuranose	HMDB
2-Deoxyadenosine	HMDB
9-(2-Deoxy-b-D-erythro-pentofuranosyl)-9H-purin-6-amine	HMDB
9-(2-Deoxy-beta-D-erythro-pentofuranosyl)-9H-purin-6-amine	HMDB
9-(2-Deoxy-beta-delta-erythro-pentofuranosyl)-9H-purin-6-amine	HMDB
9-(2-Deoxy-beta-delta-erythro-pentofuranosyl)adenine	HMDB
9-(2-Deoxy-beta-delta-ribofuranosyl)-9H-purin-6-amine	HMDB
Adenine deoxyribose	HMDB
Adenine-9 2-deoxy-b-D-erythro-pentofuranoside	HMDB
Adenine-9 2-deoxy-beta-D-erythro-pentofuranoside	HMDB
Adenine-9 2-deoxy-beta-delta-erythro-pentofuranoside	HMDB
Desoxyadenosine	HMDB
Deoxyadenosine	ChEBI

Molecular Formula

C₁₀H₁₃N₅O₃

Average Mass

251.2419

Monoisotopic Mass

251.101839307

IUPAC Name

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

Traditional Name

2-deoxyadenosine

CAS Registry Number

Not Available

SMILES

NC1=C2N=CN([C@H]3C[C@H](O)[C@@H](CO)O3)C2=NC=N1

InChI Identifier

InChI=1S/C10H13N5O3/c11-9-8-10(13-3-12-9)15(4-14-8)7-1-5(17)6(2-16)18-7/h3-7,16-17H,1-2H2,(H2,11,12,13)/t5-,6+,7+/m0/s1

InChI Key

OLXZPDWKRNYJJZ-RRKCRQDMSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as purine 2'-deoxyribonucleosides. Purine 2'-deoxyribonucleosides are compounds consisting of a purine linked to a ribose which lacks a hydroxyl group at position 2.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Purine nucleosides

Sub Class

Purine 2'-deoxyribonucleosides

Direct Parent

Purine 2'-deoxyribonucleosides

Alternative Parents

Substituents

Purine 2'-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

purine 2'-deoxyribonucleoside (CHEBI:17256 )
Deoxyribonucleosides (C00559 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	10.7 g/L	ALOGPS
logP	-0.95	ALOGPS
logP	-1.2	ChemAxon
logS	-1.4	ALOGPS
pKa (Strongest Acidic)	13.89	ChemAxon
pKa (Strongest Basic)	3.94	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	61.68 m³·mol⁻¹	ChemAxon
Polarizability	24.24 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Not Available

Biological Properties

Cellular Locations

Cytoplasm
Extracellular
Lysosome
Nucleus

Biospecimen Locations

All Tissues
Blood
Feces
Urine

Tissue Locations

All Tissues

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species
MMDBp0191677	5'-nucleotidase	Unknown	P21589	Homo sapiens
MMDBp0191680	Cytosolic 5'-nucleotidase 1B	Unknown	Q96P26	Homo sapiens
MMDBp0191681	Cytosolic 5'-nucleotidase 1A	Unknown	Q9BXI3	Homo sapiens
MMDBp0191682	5'(3')-deoxyribonucleotidase, cytosolic type	Unknown	Q8TCD5	Homo sapiens
MMDBp0191684	5'(3')-deoxyribonucleotidase, mitochondrial	Unknown	Q9NPB1	Homo sapiens
MMDBp0192304	Adenosine deaminase	Enzyme	P00813	Homo sapiens
MMDBp0193860	Cytosolic 5'-nucleotidase 3	Enzyme	Q9H0P0	Homo sapiens
MMDBp0193932	Cytosolic purine 5'-nucleotidase	Unknown	P49902	Homo sapiens
MMDBp0193933	Purine nucleoside phosphorylase	Enzyme	P00491	Homo sapiens

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0019317	Deoxyinosine	Deoxyadenosine	Adenosine deaminase	Hydrolytic deamination	PathBank	31602464
MMDBr0019318	Deoxyadenosine	Adenine	Purine nucleoside phosphorylase DeoD-type	Phosphorylation	PathBank	31602464
MMDBr0020027	S-Adenosylmethionine	L-Methionine	Lipoyl synthase, mitochondrial	Synthesis	PathBank	31602464
MMDBr0020028	S-Adenosylmethionine	L-Methionine	Lipoyl synthase, mitochondrial	Synthesis	PathBank	31602464
MMDBr0024743	Deoxyadenosine	Deoxyadenosine monophosphate	Deoxyadenosine kinase	Phosphorylation	RHEA	34755880
MMDBr0024827	Deoxyadenosine	Adenine	Purine nucleoside phosphorylase DeoD-type	Phosphorylation	RHEA	34755880
MMDBr0024831	Deoxyadenosine	Deoxyinosine	Adenosine deaminase	Hydrolytic deamination	RHEA	34755880
MMDBr0024832	Deoxyadenosine	Deoxyinosine	Adenosine deaminase	Hydrolytic deamination	RHEA	34755880
MMDBr0024845	Deoxyadenosine monophosphate	Deoxyadenosine	5'-nucleotidase SurE 1	Hydrolysis of bond; Hydrolysis of nucleotide	RHEA	34755880
MMDBr0025971	dATP	Deoxyadenosine	dATP triphosphohydrolase	Hydrolysis of bond	RHEA	34755880
MMDBr0025972	Water	Deoxyadenosine	dATP triphosphohydrolase	Hydrolysis of bond	RHEA	34755880
MMDBr0026006	2'-Deoxyadenosine 3'-phosphate	Deoxyadenosine	Polynucleotide kinase	Phosphorylation	RHEA	34755880
MMDBr0026073	Deoxyadenosine monophosphate	Deoxyadenosine	5'-nucleotidase SurE 1	Hydrolysis of nucleotide	RHEA	34755880

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference
Adenosine deaminase deficiency	Decreased	Association	Human Urine	HMDB	9869364
Adenosine deaminase deficiency	Increased	Association	Human Urine	HMDB	3436096
Adenosine deaminase deficiency	Increased	Association	Human Urine	HMDB	10102915
Adenylosuccinate lyase deficiency	Increased	Association	Human Urine	HMDB	27504266
Eosinophilic esophagitis	Slight Decrease	Association	Human Urine	HMDB	Slae, M., Huynh, H., Wishart, D.S. (2014). Analysis of 30 normal pediatric urine samples via NMR spectroscopy (unpublished work)

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria/Eubacteria	Bacteroidetes	247	Human stool; Human feces; Human urine; Human ; Human appendix biopsy; Human saliva; Human gastric fluid; Human subgingival plaque; Human supragingival plaque	Indirect association between microbiota composition and metabolites measured in host biospecimen; Metabolic reconstruction
Bacteria/Eubacteria	Firmicutes	557	Human stool; Human ; Human feces; Human pleural fluid plaque; Pig ; Human urine; Human mucosa; Human sputum; Human saliva; Human supragingival plaque; Cattle ; Human subgingival plaque	Indirect association between microbiota composition and metabolites measured in host biospecimen; Metabolic reconstruction
Bacteria/Eubacteria	Proteobacteria	535	Human feces; Human sputum; Human ; Human unknown; Pig ; Human pleural fluid plaque; Human dental plaque; Human nasal swab; Human stool; Human feces; pleural fluid plaque; bal; Rat ; Sheep ; River trout ; Cattle	Metabolic reconstruction
Bacteria	Actinobacteria	25	Human feces; Human sputum; Human bronchial brush; Human nasopharyngeal swab; Human pleural fluid plaque; Human dental plaque; Human ; Human mucosa; Human supragingival plaque; Human subgingival plaque; Human saliva; Cattle	Metabolic reconstruction
Bacteria/Eubacteria	Actinobacteria	182	Human feces; Human sputum; Human bronchial brush; Human nasopharyngeal swab; Human pleural fluid plaque; Human dental plaque; Human ; Human mucosa; Human supragingival plaque; Human subgingival plaque; Human saliva; Cattle	Metabolic reconstruction
Bacteria/Eubacteria	Verrucomicrobia	2	Human ; Human feces	Metabolic reconstruction
Bacteria/Eubacteria	Synergistetes	4	Human feces	Metabolic reconstruction
Bacteria	Firmicutes	39	Human stool; Human ; Human feces; Human pleural fluid plaque; Pig ; Human urine; Human mucosa; Human sputum; Human saliva; Human supragingival plaque; Cattle ; Human subgingival plaque	Indirect association between microbiota composition and metabolites measured in host biospecimen; Metabolic reconstruction
Bacteria	Proteobacteria	17	Human feces; Human sputum; Human ; Human unknown; Pig ; Human pleural fluid plaque; Human dental plaque; Human nasal swab; Human stool; Human feces; pleural fluid plaque; bal; Rat ; Sheep ; River trout ; Cattle	Metabolic reconstruction
Bacteria/Eubacteria	Spirochaetes	6	Human feces; Human	Metabolic reconstruction
Archaea	Thaumarchaeota	2		Metabolic reconstruction
Bacteria/Eubacteria	Fusobacteria	29	Human feces; Human	Metabolic reconstruction
Archaea	Euryarchaeota	9		Metabolic reconstruction
Bacteria	Candidatus melainabacteria	2	Human feces	Metabolic reconstruction
Bacteria/Eubacteria	Tenericutes	7	Human feces	Metabolic reconstruction
Bacteria/Eubacteria	Planctomycetes	3	Human feces	Metabolic reconstruction
Archaea	Crenarchaeota	2		Metabolic reconstruction
Bacteria	Synergistetes	1	Human feces	Metabolic reconstruction
Eukaryota/Fungi	Basidiomycota	1	Human feces
Eukaryota/Fungi	Ascomycota	5	Human feces; Human saliva	Unknown
Archaea/Archaea	Euryarchaeota	26		Metabolic reconstruction
Archaea/Archaea	Crenarchaeota	4		Metabolic reconstruction
Bacteria/Eubacteria	Aquificae	1
Bacteria/Eubacteria	Chlorobi	8
Bacteria/Eubacteria	Cyanobacteria	17
Archaea	Euryarchaeota	1
Bacteria/Eubacteria	Acidobacteria	1
Bacteria	nah	2
Bacteria/Eubacteria	Thermotogae	1
Bacteria/Eubacteria	Deinococcus-thermus	1

Exposure Sources

Food Exposures

Other Exposures

Source Type	Data Source	Reference
Cosmetics	U.S. Environmental Protection Agency	CompTox
Domestics	U.S. Environmental Protection Agency	CompTox
Domestics	U.S. Environmental Protection Agency	CompTox

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference
Human Feces	Detected but not Quantified									HMDB
Human Urine	Detected and Quantified	0.005		0.000	0.010	umol/mmol creatinine	Adult (>18 years old)	Both	Adenosine deaminase(ADA) deficiency	HMDB	9869364
Human Urine	Detected and Quantified			10	190	umol/mmol creatinine	Infant (0-1 year old)	Not Specified	Adenosine deaminase (ADA) deficiency	HMDB	3436096
Human Urine	Detected and Quantified	176.0		167.0	185.0	umol/mmol creatinine	Adult (>18 years old)	Both	Adenosine deaminase(ADA) deficiency	HMDB	10102915
Human Urine	Detected and Quantified			2	7.2	umol/mmol creatinine	Infant (0-1 year old)	Both	Adenylosuccinase deficiency	HMDB	27504266
Human Urine	Detected and Quantified	<0.1				umol/mmol creatinine	Infant (0-1 year old)	Both	Normal	HMDB	30817767
Human Urine	Detected and Quantified	<1				umol/mmol creatinine	Infant (0-1 year old)	Not Specified	Normal	HMDB	3436096
Human Urine	Detected and Quantified			0	3.2	umol/mmol creatinine	Adult (>18 years old)	Not Specified	Normal	HMDB	27504266
Human Urine	Detected and Quantified			0	4.1	umol/mmol creatinine	Infant (0-1 year old)	Not Specified	Normal	HMDB	27504266
Human Urine	Detected and Quantified	0.22	0.09			umol/mmol creatinine	Adult (>18 years old)	Both	Normal	HMDB	9869364
Human Urine	Detected and Quantified	8.318	9.422			umol/mmol creatinine	Children (1 - 13 years old)	Not Specified	Eosinophilic esophagitis	HMDB	Analysis of 30 normal pediatric urine samples via NMR spectroscopy (unpublished work)
Human Urine	Detected and Quantified	13.002	4.766			umol/mmol creatinine	Children (1 - 13 years old)	Not Specified	Normal	HMDB	Analysis of 30 normal pediatric urine samples via NMR spectroscopy (unpublished work)
Human Urine	Detected and Quantified			0	8	umol/mmol creatinine	Children (1 - 18 years old)	Both	Normal	HMDB	BC Children's Hospital Biochemical Genetics Lab
Human All tissues	Detected but not Quantified						Not Specified	Not Specified	Normal	HMDB	34986597
Human Feces	Detected but not Quantified						Adult (>18 years old)	Both	Normal	HMDB	27543620
Human Feces	Detected but not Quantified						Adult (>18 years old)	Both	Normal	HMDB	25037050
Human Feces	Detected but not Quantified						Adult (>18 years old)	Both	Normal	HMDB	29808030
Human Blood	Detected but not Quantified									HMDB

External Links

HMDB ID

HMDB0000101

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Wikipedia Link

METLIN ID

PubChem Compound

PDB ID

Not Available

ChEBI ID

17256

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Sheridan W, Gordon DS, Fullen AJ, Olson A, Vogler WR, Winton E: Preclinical studies on deoxycoformycin and deoxyadenosine as pharmacologic T cell purging tools. Bone Marrow Transplant. 1989 Sep;4(5):511-7. [PubMed:2790329 ]
Carson DA, Carrera CJ, Kubota M, Wasson DB, Iizasa T: Genetic analysis of deoxyadenosine toxicity in dividing human lymphoblasts. Adv Exp Med Biol. 1986;195 Pt B:207-11. doi: 10.1007/978-1-4684-1248-2_31. [PubMed:3020905 ]
Mitchell BS, Edwards NL: Purine metabolizing enzymes as predictors of lymphoblast sensitivity to deoxyadenosine. J Lab Clin Med. 1984 Sep;104(3):414-24. [PubMed:6147383 ]
Carson DA, Wasson DB, Kaye J, Ullman B, Martin DW Jr, Robins RK, Montgomery JA: Deoxycytidine kinase-mediated toxicity of deoxyadenosine analogs toward malignant human lymphoblasts in vitro and toward murine L1210 leukemia in vivo. Proc Natl Acad Sci U S A. 1980 Nov;77(11):6865-9. doi: 10.1073/pnas.77.11.6865. [PubMed:6256765 ]
Fox RM, Tripp EH, Taylor IW: Analytical DNA flow cytometric analysis of deoxyadenosine toxicity in cultured human leukemic lymphoblasts. Mol Pharmacol. 1984 Sep;26(2):388-94. [PubMed:6332978 ]
Hershfield MS, Kredich NM, Koller CA, Mitchell BS, Kurtzberg J, Kinney TR, Falletta JM: S-adenosylhomocysteine catabolism and basis for acquired resistance during treatment of T-cell acute lymphoblastic leukemia with 2'-deoxycoformycin alone and in combination with 9-beta-D-arabinofuranosyladenine. Cancer Res. 1983 Jul;43(7):3451-8. [PubMed:6601986 ]
Webster DR, Simmonds HA, Perrett D, Levinsky RJ: Nucleotide levels and metabolism of adenosine and deoxyadenosine in intact erythrocytes deficient in adenosine deaminase. Adv Exp Med Biol. 1984;165 Pt A:363-6. doi: 10.1007/978-1-4684-4553-4_72. [PubMed:6609529 ]
Bluestein HG, Thompson LF, Albert DA, Seegmiller JE: Altered deoxynucleoside triphosphate levels paralleling deoxyadenosine toxicity in adenosine deaminase inhibited human lymphocytes. Adv Exp Med Biol. 1980;122A:427-31. doi: 10.1007/978-1-4615-9140-5_69. [PubMed:6968502 ]
Hayward AR: Resistance of pokeweed mitogen-stimulated B cells to inhibition by deoxyadenosine. Clin Exp Immunol. 1980 Jul;41(1):141-9. [PubMed:6969149 ]
Brox LW, Pollock E, Belch A: Adenosine and deoxyadenosine toxicity in colony assay systems for human T-lymphocytes, B-lymphocytes, and granulocytes. Cancer Chemother Pharmacol. 1982;9(1):49-52. doi: 10.1007/BF00296762. [PubMed:6982786 ]
Juliusson G, Liliemark J: High complete remission rate from 2-chloro-2'-deoxyadenosine in previously treated patients with B-cell chronic lymphocytic leukemia: response predicted by rapid decrease of blood lymphocyte count. J Clin Oncol. 1993 Apr;11(4):679-89. doi: 10.1200/JCO.1993.11.4.679. [PubMed:8097528 ]
Szabados E, Christopherson RI: Rapid radioassay for metabolites of adenosine and deoxyadenosine in erythrocytes. J Chromatogr B Biomed Appl. 1995 Dec 1;674(1):132-7. doi: 10.1016/0378-4347(95)00288-x. [PubMed:8749261 ]
Yamamoto T, Moriwaki Y, Takahashi S, Fujita T, Tsutsumi Z, Yamakita J, Shimizu K, Shiota M, Ohta S, Higashino K: Determination of adenosine and deoxyadenosine in urine by high-performance liquid chromatography with column switching. J Chromatogr B Biomed Sci Appl. 1998 Nov 20;719(1-2):55-61. doi: 10.1016/s0378-4347(98)00402-2. [PubMed:9869364 ]
Wevers RA, Engelke UF, Moolenaar SH, Brautigam C, de Jong JG, Duran R, de Abreu RA, van Gennip AH: 1H-NMR spectroscopy of body fluids: inborn errors of purine and pyrimidine metabolism. Clin Chem. 1999 Apr;45(4):539-48. [PubMed:10102915 ]

Showing metabocard for Deoxyadenosine (MMDBc0000334)

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