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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-11 14:54:19 UTC

Update Date

2021-09-26 23:09:58 UTC

HMDB ID

HMDB0255300

Secondary Accession Numbers

None

Metabolite Identification

Common Name

N6-Methyl-2'-deoxyadenosine

Description

Adenosine,2'-deoxy-N-methyl- 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. Adenosine,2'-deoxy-N-methyl- is a strong basic compound (based on its pKa). This compound has been identified in human blood as reported by (PMID: 31557052 ). N6-methyl-2'-deoxyadenosine is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically N6-Methyl-2'-deoxyadenosine 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

HMDB0255300
     RDKit          3D
N6-Methyl-2'-deoxyadenosine
 34 36  0  0  0  0  0  0  0  0999 V2000
    5.9332    0.3738    0.0449 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5400    0.5266    0.4211 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.4910   -0.1556   -0.2618 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7139   -0.9808   -1.2923 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.7400   -1.6361   -1.9530 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4688   -1.4461   -1.5483 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1801   -0.6255   -0.5143 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2055    0.0324    0.1423 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6525    0.7668    1.1083 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.3145    0.6104    1.1023 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0503   -0.2432    0.1040 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2710   -0.7024   -0.2713 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0366   -1.0408    0.9681 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0813    0.0288    1.0888 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3308   -0.5299    0.8469 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7558    0.9542   -0.0354 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0510    1.4617   -0.6279 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8343    0.4155   -1.1083 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9953    0.2692   -0.9614 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0590    0.0512   -1.0060 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4097    1.3717    0.1425 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4160   -0.3897    0.7025 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3351    1.1615    1.2187 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9869   -2.3029   -2.7949 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4245    1.0742    1.7657 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2068   -1.6139   -0.8957 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3510   -1.0865    1.8498 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4899   -2.0685    0.9030 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0499    0.5183    2.0927 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2156   -1.3693    0.3551 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1871    1.8598    0.2902 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8162    2.2184   -1.3995 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6099    1.9857    0.1721 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7897    0.5110   -0.8791 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 14 16  1  0
 16 17  1  0
 17 18  1  0
 16 19  1  0
  8  3  1  0
 19 12  1  0
 11  7  1  0
  1 20  1  0
  1 21  1  0
  1 22  1  0
  2 23  1  0
  5 24  1  0
 10 25  1  0
 12 26  1  0
 13 27  1  0
 13 28  1  0
 14 29  1  0
 15 30  1  0
 16 31  1  0
 17 32  1  0
 17 33  1  0
 18 34  1  0
M  END


  Mrv1533004251508282D          

 19 21  0  0  0  0            999 V2000
    3.9934    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    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 C   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 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
    0.0728   -2.6044    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1591   -3.4249    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7403   -1.2945    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  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  3  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
  7 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
 14 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 16 19  1  0  0  0  0
 12 19  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0255300

> <DATABASE_NAME>
hmdb

> <SMILES>
CNC1=C2N=CN(C3CC(O)C(CO)O3)C2=NC=N1

> <INCHI_IDENTIFIER>
InChI=1S/C11H15N5O3/c1-12-10-9-11(14-4-13-10)16(5-15-9)8-2-6(18)7(3-17)19-8/h4-8,17-18H,2-3H2,1H3,(H,12,13,14)

> <INCHI_KEY>
DYSDOYRQWBDGQQ-UHFFFAOYSA-N

> <FORMULA>
C11H15N5O3

> <MOLECULAR_WEIGHT>
265.273

> <EXACT_MASS>
265.117489363

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
34

> <JCHEM_AVERAGE_POLARIZABILITY>
26.86034800761478

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-(hydroxymethyl)-5-[6-(methylamino)-9H-purin-9-yl]oxolan-3-ol

> <ALOGPS_LOGP>
-0.58

> <JCHEM_LOGP>
-0.8886217273333328

> <ALOGPS_LOGS>
-1.63

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.785047120653893

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.886735217112161

> <JCHEM_PKA_STRONGEST_BASIC>
4.904318782592181

> <JCHEM_POLAR_SURFACE_AREA>
105.32000000000001

> <JCHEM_REFRACTIVITY>
67.17830000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.18e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
adenosine,2'-deoxy-N6-methyl-

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0255300
     RDKit          3D
N6-Methyl-2'-deoxyadenosine
 34 36  0  0  0  0  0  0  0  0999 V2000
    5.9332    0.3738    0.0449 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5400    0.5266    0.4211 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.4910   -0.1556   -0.2618 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7139   -0.9808   -1.2923 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.7400   -1.6361   -1.9530 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4688   -1.4461   -1.5483 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1801   -0.6255   -0.5143 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2055    0.0324    0.1423 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6525    0.7668    1.1083 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.3145    0.6104    1.1023 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0503   -0.2432    0.1040 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2710   -0.7024   -0.2713 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0366   -1.0408    0.9681 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0813    0.0288    1.0888 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3308   -0.5299    0.8469 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7558    0.9542   -0.0354 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0510    1.4617   -0.6279 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8343    0.4155   -1.1083 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9953    0.2692   -0.9614 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0590    0.0512   -1.0060 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4097    1.3717    0.1425 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4160   -0.3897    0.7025 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3351    1.1615    1.2187 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9869   -2.3029   -2.7949 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4245    1.0742    1.7657 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2068   -1.6139   -0.8957 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3510   -1.0865    1.8498 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4899   -2.0685    0.9030 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0499    0.5183    2.0927 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2156   -1.3693    0.3551 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1871    1.8598    0.2902 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8162    2.2184   -1.3995 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6099    1.9857    0.1721 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7897    0.5110   -0.8791 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 14 16  1  0
 16 17  1  0
 17 18  1  0
 16 19  1  0
  8  3  1  0
 19 12  1  0
 11  7  1  0
  1 20  1  0
  1 21  1  0
  1 22  1  0
  2 23  1  0
  5 24  1  0
 10 25  1  0
 12 26  1  0
 13 27  1  0
 13 28  1  0
 14 29  1  0
 15 30  1  0
 16 31  1  0
 17 32  1  0
 17 33  1  0
 18 34  1  0
M  END

HEADER    PROTEIN                                 25-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   25-APR-15         0                                  
HETATM    1  C   UNK     0       7.454   4.620   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0       6.121   3.850   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0       6.121   2.310   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0       7.454   1.540   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0       7.454   0.000   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0       6.121  -0.770   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0       4.787   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.787   1.540   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0       3.322   2.016   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0       2.417   0.770   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0       3.322  -0.476   0.000  0.00  0.00           N+0
HETATM   12  C   UNK     0       2.846  -1.941   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       3.752  -3.186   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       2.846  -4.432   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       3.322  -5.897   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       0.136  -4.862   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       0.297  -6.393   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       1.382  -2.416   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    8                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8   11                                                  
CONECT    8    7    3    9                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10    7   12                                                  
CONECT   12   11   13   19                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14   17   19                                                  
CONECT   17   16   18                                                       
CONECT   18   17                                                            
CONECT   19   16   12                                                       
MASTER        0    0    0    0    0    0    0    0   19    0   42    0
END

COMPND    HMDB0255300
HETATM    1  C1  UNL     1       5.933   0.374   0.045  1.00  0.00           C  
HETATM    2  N1  UNL     1       4.540   0.527   0.421  1.00  0.00           N  
HETATM    3  C2  UNL     1       3.491  -0.156  -0.262  1.00  0.00           C  
HETATM    4  N2  UNL     1       3.714  -0.981  -1.292  1.00  0.00           N  
HETATM    5  C3  UNL     1       2.740  -1.636  -1.953  1.00  0.00           C  
HETATM    6  N3  UNL     1       1.469  -1.446  -1.548  1.00  0.00           N  
HETATM    7  C4  UNL     1       1.180  -0.625  -0.514  1.00  0.00           C  
HETATM    8  C5  UNL     1       2.206   0.032   0.142  1.00  0.00           C  
HETATM    9  N4  UNL     1       1.653   0.767   1.108  1.00  0.00           N  
HETATM   10  C6  UNL     1       0.314   0.610   1.102  1.00  0.00           C  
HETATM   11  N5  UNL     1       0.050  -0.243   0.104  1.00  0.00           N  
HETATM   12  C7  UNL     1      -1.271  -0.702  -0.271  1.00  0.00           C  
HETATM   13  C8  UNL     1      -2.037  -1.041   0.968  1.00  0.00           C  
HETATM   14  C9  UNL     1      -3.081   0.029   1.089  1.00  0.00           C  
HETATM   15  O1  UNL     1      -4.331  -0.530   0.847  1.00  0.00           O  
HETATM   16  C10 UNL     1      -2.756   0.954  -0.035  1.00  0.00           C  
HETATM   17  C11 UNL     1      -4.051   1.462  -0.628  1.00  0.00           C  
HETATM   18  O2  UNL     1      -4.834   0.416  -1.108  1.00  0.00           O  
HETATM   19  O3  UNL     1      -1.995   0.269  -0.961  1.00  0.00           O  
HETATM   20  H1  UNL     1       6.059   0.051  -1.006  1.00  0.00           H  
HETATM   21  H2  UNL     1       6.410   1.372   0.143  1.00  0.00           H  
HETATM   22  H3  UNL     1       6.416  -0.390   0.703  1.00  0.00           H  
HETATM   23  H4  UNL     1       4.335   1.162   1.219  1.00  0.00           H  
HETATM   24  H5  UNL     1       2.987  -2.303  -2.795  1.00  0.00           H  
HETATM   25  H6  UNL     1      -0.425   1.074   1.766  1.00  0.00           H  
HETATM   26  H7  UNL     1      -1.207  -1.614  -0.896  1.00  0.00           H  
HETATM   27  H8  UNL     1      -1.351  -1.087   1.850  1.00  0.00           H  
HETATM   28  H9  UNL     1      -2.490  -2.069   0.903  1.00  0.00           H  
HETATM   29  H10 UNL     1      -3.050   0.518   2.093  1.00  0.00           H  
HETATM   30  H11 UNL     1      -4.216  -1.369   0.355  1.00  0.00           H  
HETATM   31  H12 UNL     1      -2.187   1.860   0.290  1.00  0.00           H  
HETATM   32  H13 UNL     1      -3.816   2.218  -1.399  1.00  0.00           H  
HETATM   33  H14 UNL     1      -4.610   1.986   0.172  1.00  0.00           H  
HETATM   34  H15 UNL     1      -5.790   0.511  -0.879  1.00  0.00           H  
CONECT    1    2   20   21   22
CONECT    2    3   23
CONECT    3    4    4    8
CONECT    4    5
CONECT    5    6    6   24
CONECT    6    7
CONECT    7    8    8   11
CONECT    8    9
CONECT    9   10   10
CONECT   10   11   25
CONECT   11   12
CONECT   12   13   19   26
CONECT   13   14   27   28
CONECT   14   15   16   29
CONECT   15   30
CONECT   16   17   19   31
CONECT   17   18   32   33
CONECT   18   34
END

HMDB0255300
     RDKit          3D
N6-Methyl-2'-deoxyadenosine
 34 36  0  0  0  0  0  0  0  0999 V2000
    5.9332    0.3738    0.0449 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5400    0.5266    0.4211 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.4910   -0.1556   -0.2618 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7139   -0.9808   -1.2923 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.7400   -1.6361   -1.9530 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4688   -1.4461   -1.5483 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1801   -0.6255   -0.5143 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2055    0.0324    0.1423 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6525    0.7668    1.1083 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.3145    0.6104    1.1023 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0503   -0.2432    0.1040 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2710   -0.7024   -0.2713 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0366   -1.0408    0.9681 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0813    0.0288    1.0888 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3308   -0.5299    0.8469 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7558    0.9542   -0.0354 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0510    1.4617   -0.6279 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8343    0.4155   -1.1083 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9953    0.2692   -0.9614 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0590    0.0512   -1.0060 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4097    1.3717    0.1425 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4160   -0.3897    0.7025 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3351    1.1615    1.2187 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9869   -2.3029   -2.7949 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4245    1.0742    1.7657 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2068   -1.6139   -0.8957 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3510   -1.0865    1.8498 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4899   -2.0685    0.9030 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0499    0.5183    2.0927 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2156   -1.3693    0.3551 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1871    1.8598    0.2902 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8162    2.2184   -1.3995 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6099    1.9857    0.1721 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7897    0.5110   -0.8791 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 14 16  1  0
 16 17  1  0
 17 18  1  0
 16 19  1  0
  8  3  1  0
 19 12  1  0
 11  7  1  0
  1 20  1  0
  1 21  1  0
  1 22  1  0
  2 23  1  0
  5 24  1  0
 10 25  1  0
 12 26  1  0
 13 27  1  0
 13 28  1  0
 14 29  1  0
 15 30  1  0
 16 31  1  0
 17 32  1  0
 17 33  1  0
 18 34  1  0
M  END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Not Available

Chemical Formula

C₁₁H₁₅N₅O₃

Average Molecular Weight

265.273

Monoisotopic Molecular Weight

265.117489363

IUPAC Name

2-(hydroxymethyl)-5-[6-(methylamino)-9H-purin-9-yl]oxolan-3-ol

Traditional Name

adenosine,2'-deoxy-N6-methyl-

CAS Registry Number

Not Available

SMILES

CNC1=C2N=CN(C3CC(O)C(CO)O3)C2=NC=N1

InChI Identifier

InChI=1S/C11H15N5O3/c1-12-10-9-11(14-4-13-10)16(5-15-9)8-2-6(18)7(3-17)19-8/h4-8,17-18H,2-3H2,1H3,(H,12,13,14)

InChI Key

DYSDOYRQWBDGQQ-UHFFFAOYSA-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-alkylaminopurine
6-aminopurine
Imidazopyrimidine
Purine
Aminopyrimidine
Secondary aliphatic/aromatic amine
N-substituted imidazole
Pyrimidine
Imidolactam
Tetrahydrofuran
Heteroaromatic compound
Azole
Imidazole
Secondary alcohol
Secondary amine
Oxacycle
Organoheterocyclic compound
Azacycle
Alcohol
Organonitrogen compound
Organic nitrogen compound
Organopnictogen compound
Organooxygen compound
Primary alcohol
Organic oxygen compound
Hydrocarbon derivative
Amine
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Ontology

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	-0.58	ALOGPS
logP	-0.89	ChemAxon
logS	-1.6	ALOGPS
pKa (Strongest Acidic)	13.89	ChemAxon
pKa (Strongest Basic)	4.9	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	105.32 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	67.18 m³·mol⁻¹	ChemAxon
Polarizability	26.86 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]+	161.11	30932474
DeepCCS	[M-H]-	158.752	30932474
DeepCCS	[M-2H]-	191.638	30932474
DeepCCS	[M+Na]+	167.203	30932474
AllCCS	[M+H]+	162.0	32859911
AllCCS	[M+H-H2O]+	158.4	32859911
AllCCS	[M+NH4]+	165.3	32859911
AllCCS	[M+Na]+	166.3	32859911
AllCCS	[M-H]-	162.2	32859911
AllCCS	[M+Na-2H]-	161.9	32859911
AllCCS	[M+HCOO]-	161.7	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
N6-Methyl-2'-deoxyadenosine	CNC1=C2N=CN(C3CC(O)C(CO)O3)C2=NC=N1	3225.2	Standard polar	33892256
N6-Methyl-2'-deoxyadenosine	CNC1=C2N=CN(C3CC(O)C(CO)O3)C2=NC=N1	2369.0	Standard non polar	33892256
N6-Methyl-2'-deoxyadenosine	CNC1=C2N=CN(C3CC(O)C(CO)O3)C2=NC=N1	2631.3	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
N6-Methyl-2'-deoxyadenosine,3TMS,isomer #1	CN(C1=NC=NC2=C1N=CN2C1CC(O[Si](C)(C)C)C(CO[Si](C)(C)C)O1)[Si](C)(C)C	2572.3	Semi standard non polar	33892256
N6-Methyl-2'-deoxyadenosine,3TMS,isomer #1	CN(C1=NC=NC2=C1N=CN2C1CC(O[Si](C)(C)C)C(CO[Si](C)(C)C)O1)[Si](C)(C)C	2682.6	Standard non polar	33892256
N6-Methyl-2'-deoxyadenosine,3TMS,isomer #1	CN(C1=NC=NC2=C1N=CN2C1CC(O[Si](C)(C)C)C(CO[Si](C)(C)C)O1)[Si](C)(C)C	3316.5	Standard polar	33892256
N6-Methyl-2'-deoxyadenosine,3TBDMS,isomer #1	CN(C1=NC=NC2=C1N=CN2C1CC(O[Si](C)(C)C(C)(C)C)C(CO[Si](C)(C)C(C)(C)C)O1)[Si](C)(C)C(C)(C)C	3142.9	Semi standard non polar	33892256
N6-Methyl-2'-deoxyadenosine,3TBDMS,isomer #1	CN(C1=NC=NC2=C1N=CN2C1CC(O[Si](C)(C)C(C)(C)C)C(CO[Si](C)(C)C(C)(C)C)O1)[Si](C)(C)C(C)(C)C	3366.4	Standard non polar	33892256
N6-Methyl-2'-deoxyadenosine,3TBDMS,isomer #1	CN(C1=NC=NC2=C1N=CN2C1CC(O[Si](C)(C)C(C)(C)C)C(CO[Si](C)(C)C(C)(C)C)O1)[Si](C)(C)C(C)(C)C	3496.9	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - N6-Methyl-2'-deoxyadenosine GC-MS (Non-derivatized) - 70eV, Positive	splash10-0006-9370000000-8b1dad784809bc50c894	2021-09-23	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - N6-Methyl-2'-deoxyadenosine GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - N6-Methyl-2'-deoxyadenosine GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - N6-Methyl-2'-deoxyadenosine GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - N6-Methyl-2'-deoxyadenosine GC-MS (TMS_1_3) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - N6-Methyl-2'-deoxyadenosine GC-MS (TMS_2_1) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - N6-Methyl-2'-deoxyadenosine GC-MS (TMS_2_2) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - N6-Methyl-2'-deoxyadenosine GC-MS (TMS_2_3) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - N6-Methyl-2'-deoxyadenosine GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - N6-Methyl-2'-deoxyadenosine GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - N6-Methyl-2'-deoxyadenosine GC-MS (TBDMS_1_3) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - N6-Methyl-2'-deoxyadenosine GC-MS (TBDMS_2_1) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - N6-Methyl-2'-deoxyadenosine GC-MS (TBDMS_2_2) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - N6-Methyl-2'-deoxyadenosine GC-MS (TBDMS_2_3) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-10-25	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

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

248869

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 ]

Showing metabocard for N6-Methyl-2'-deoxyadenosine (HMDB0255300)

MOL for HMDB0255300 (N6-Methyl-2'-deoxyadenosine)

3D MOL for HMDB0255300 (N6-Methyl-2'-deoxyadenosine)

3D SDF for HMDB0255300 (N6-Methyl-2'-deoxyadenosine)

3D-SDF for HMDB0255300 (N6-Methyl-2'-deoxyadenosine)

PDB for HMDB0255300 (N6-Methyl-2'-deoxyadenosine)

3D PDB for HMDB0255300 (N6-Methyl-2'-deoxyadenosine)

SMILES for HMDB0255300 (N6-Methyl-2'-deoxyadenosine)

INCHI for HMDB0255300 (N6-Methyl-2'-deoxyadenosine)

Structure for HMDB0255300 (N6-Methyl-2'-deoxyadenosine)

3D Structure for HMDB0255300 (N6-Methyl-2'-deoxyadenosine)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

NMR Spectra