MiMeDB: Showing metabocard for 5'-Deoxyadenosine (MMDBc0030308)

Plant

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-18 00:02:44 UTC

Update Date

2022-08-31 17:43:30 UTC

Metabolite ID

MMDBc0030308

Metabolite Identification

Common Name

5'-Deoxyadenosine

Description

5'-Deoxyadenosine is an abnormal form of deoxyadenosine derived from S-adenosylmethionine. The normal form of deoxyadenosine used in DNA synthesis and repair is 2'-deoxyadenosine where the hydroxyl group (-OH) is at the 2' position of its ribose sugar moiety. 5'-deoxyadenosine has its hydroxyl group at the 5' position of the ribose sugar. 5'-deoxyadenosine is a substrate for 5'-methylthioadenosine phosphorylase. It is also a product of the degradation/conversion of S-adenosyl-methionine by the enzymes: 2-iminoacetate synthase, biotin synthase, lopoyl synthase and pyruvate-formate lyase activating enzyme

Structure

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

HMDB0001983
     RDKit          3D
5'-Deoxyadenosine
 31 33  0  0  0  0  0  0  0  0999 V2000
   -3.5821   -0.2285   -1.5338 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6570   -0.5382   -0.3915 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.4046   -0.9559   -0.8088 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6726   -1.0021    0.3807 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7502   -0.9763    0.1435 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.5572   -2.0691    0.0983 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8109   -1.6467   -0.1429 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.8099   -0.3087   -0.2507 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7953    0.6347   -0.4896 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1332    0.1912   -0.6750 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.4548    1.9282   -0.5376 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1908    2.3382   -0.3618 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2280    1.4290   -0.1294 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.5209    0.1051   -0.0710 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1603    0.1063    1.2534 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.7892   -0.4122    2.4092 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3046    0.6907    0.4145 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.3360    1.1482    1.1901 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1629    0.4693   -2.2747 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5169    0.1831   -1.0946 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8760   -1.2098   -1.9826 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1014   -1.3272    0.2189 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9421   -1.9920    0.8513 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2107   -3.0957    0.2384 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3157   -0.3939   -1.5333 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8559    0.4505    0.0173 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9941    3.3989   -0.4148 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4190    0.8599    1.5089 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5289   -1.3720    2.5030 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8497    1.4379   -0.2510 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3239    2.1571    1.1406 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
 15 17  1  0
 17 18  1  0
 17  2  1  0
 14  5  1  0
 14  8  1  0
  1 19  1  0
  1 20  1  0
  1 21  1  0
  2 22  1  1
  4 23  1  1
  6 24  1  0
 10 25  1  0
 10 26  1  0
 12 27  1  0
 15 28  1  1
 16 29  1  0
 17 30  1  6
 18 31  1  0
M  END


  Mrv1652309042000252D          

 18 20  0  0  0  0            999 V2000
    6.0924    1.6396    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.0924    0.8146    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3780    0.4021    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.3779   -0.4229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0923   -0.8354    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.8069   -0.4229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8069    0.4021    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.5915    0.6570    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    8.0765   -0.0105    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.5915   -0.6778    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    7.8465   -1.4626    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    7.3615   -2.1300    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.8464   -2.7976    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    7.5914   -3.5822    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.6310   -2.5425    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    9.2985   -3.0276    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.6311   -1.7176    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    9.2985   -1.2326    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
  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 17  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  1  0  0  0
 13 15  1  0  0  0  0
 15 16  1  6  0  0  0
 15 17  1  0  0  0  0
 17 18  1  6  0  0  0
M  END
> <DATABASE_ID>
MMDBc0030308

> <DATABASE_NAME>
MIME

> <SMILES>
C[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C=NC2=C(N)N=CN=C12

> <INCHI_IDENTIFIER>
InChI=1S/C10H13N5O3/c1-4-6(16)7(17)10(18-4)15-3-14-5-8(11)12-2-13-9(5)15/h2-4,6-7,10,16-17H,1H3,(H2,11,12,13)/t4-,6-,7-,10-/m1/s1

> <INCHI_KEY>
XGYIMTFOTBMPFP-KQYNXXCUSA-N

> <FORMULA>
C10H13N5O3

> <MOLECULAR_WEIGHT>
251.2419

> <EXACT_MASS>
251.101839307

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
31

> <JCHEM_AVERAGE_POLARIZABILITY>
24.30241412668001

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3R,4S,5R)-2-(6-amino-9H-purin-9-yl)-5-methyloxolane-3,4-diol

> <ALOGPS_LOGP>
-0.52

> <JCHEM_LOGP>
-1.0440539050000002

> <ALOGPS_LOGS>
-1.41

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.04065367928522

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.482511642166756

> <JCHEM_PKA_STRONGEST_BASIC>
3.9212963575149358

> <JCHEM_POLAR_SURFACE_AREA>
119.30999999999999

> <JCHEM_REFRACTIVITY>
61.6519

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
9.88e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5'-deoxyadenosine

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0001983
     RDKit          3D
5'-Deoxyadenosine
 31 33  0  0  0  0  0  0  0  0999 V2000
   -3.5821   -0.2285   -1.5338 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6570   -0.5382   -0.3915 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.4046   -0.9559   -0.8088 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6726   -1.0021    0.3807 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7502   -0.9763    0.1435 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.5572   -2.0691    0.0983 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8109   -1.6467   -0.1429 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.8099   -0.3087   -0.2507 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7953    0.6347   -0.4896 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1332    0.1912   -0.6750 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.4548    1.9282   -0.5376 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1908    2.3382   -0.3618 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2280    1.4290   -0.1294 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.5209    0.1051   -0.0710 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1603    0.1063    1.2534 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.7892   -0.4122    2.4092 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3046    0.6907    0.4145 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.3360    1.1482    1.1901 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1629    0.4693   -2.2747 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5169    0.1831   -1.0946 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8760   -1.2098   -1.9826 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1014   -1.3272    0.2189 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9421   -1.9920    0.8513 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2107   -3.0957    0.2384 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3157   -0.3939   -1.5333 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8559    0.4505    0.0173 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9941    3.3989   -0.4148 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4190    0.8599    1.5089 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5289   -1.3720    2.5030 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8497    1.4379   -0.2510 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3239    2.1571    1.1406 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
 15 17  1  0
 17 18  1  0
 17  2  1  0
 14  5  1  0
 14  8  1  0
  1 19  1  0
  1 20  1  0
  1 21  1  0
  2 22  1  1
  4 23  1  1
  6 24  1  0
 10 25  1  0
 10 26  1  0
 12 27  1  0
 15 28  1  1
 16 29  1  0
 17 30  1  6
 18 31  1  0
M  END

HEADER    PROTEIN                                 04-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-20         0                                  
HETATM    1  N   UNK     0      11.372   3.061   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0      11.372   1.521   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0      10.039   0.751   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0      10.039  -0.789   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0      11.372  -1.559   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0      12.706  -0.789   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      12.706   0.751   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0      14.171   1.226   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0      15.076  -0.020   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0      14.171  -1.265   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0      14.647  -2.730   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      13.741  -3.976   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      14.647  -5.222   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      14.171  -6.687   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      16.111  -4.746   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      17.357  -5.652   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0      16.111  -3.206   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      17.357  -2.301   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    7                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7   10                                                  
CONECT    7    2    6    8                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    6    9   11                                                  
CONECT   11   10   12   17                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16   17                                                  
CONECT   16   15                                                            
CONECT   17   11   15   18                                                  
CONECT   18   17                                                            
MASTER        0    0    0    0    0    0    0    0   18    0   40    0
END

COMPND    HMDB0001983
HETATM    1  C1  UNL     1      -3.582  -0.228  -1.534  1.00  0.00           C  
HETATM    2  C2  UNL     1      -2.657  -0.538  -0.392  1.00  0.00           C  
HETATM    3  O1  UNL     1      -1.405  -0.956  -0.809  1.00  0.00           O  
HETATM    4  C3  UNL     1      -0.673  -1.002   0.381  1.00  0.00           C  
HETATM    5  N1  UNL     1       0.750  -0.976   0.144  1.00  0.00           N  
HETATM    6  C4  UNL     1       1.557  -2.069   0.098  1.00  0.00           C  
HETATM    7  N2  UNL     1       2.811  -1.647  -0.143  1.00  0.00           N  
HETATM    8  C5  UNL     1       2.810  -0.309  -0.251  1.00  0.00           C  
HETATM    9  C6  UNL     1       3.795   0.635  -0.490  1.00  0.00           C  
HETATM   10  N3  UNL     1       5.133   0.191  -0.675  1.00  0.00           N  
HETATM   11  N4  UNL     1       3.455   1.928  -0.538  1.00  0.00           N  
HETATM   12  C7  UNL     1       2.191   2.338  -0.362  1.00  0.00           C  
HETATM   13  N5  UNL     1       1.228   1.429  -0.129  1.00  0.00           N  
HETATM   14  C8  UNL     1       1.521   0.105  -0.071  1.00  0.00           C  
HETATM   15  C9  UNL     1      -1.160   0.106   1.253  1.00  0.00           C  
HETATM   16  O2  UNL     1      -1.789  -0.412   2.409  1.00  0.00           O  
HETATM   17  C10 UNL     1      -2.305   0.691   0.414  1.00  0.00           C  
HETATM   18  O3  UNL     1      -3.336   1.148   1.190  1.00  0.00           O  
HETATM   19  H1  UNL     1      -3.163   0.469  -2.275  1.00  0.00           H  
HETATM   20  H2  UNL     1      -4.517   0.183  -1.095  1.00  0.00           H  
HETATM   21  H3  UNL     1      -3.876  -1.210  -1.983  1.00  0.00           H  
HETATM   22  H4  UNL     1      -3.101  -1.327   0.219  1.00  0.00           H  
HETATM   23  H5  UNL     1      -0.942  -1.992   0.851  1.00  0.00           H  
HETATM   24  H6  UNL     1       1.211  -3.096   0.238  1.00  0.00           H  
HETATM   25  H7  UNL     1       5.316  -0.394  -1.533  1.00  0.00           H  
HETATM   26  H8  UNL     1       5.856   0.451   0.017  1.00  0.00           H  
HETATM   27  H9  UNL     1       1.994   3.399  -0.415  1.00  0.00           H  
HETATM   28  H10 UNL     1      -0.419   0.860   1.509  1.00  0.00           H  
HETATM   29  H11 UNL     1      -1.529  -1.372   2.503  1.00  0.00           H  
HETATM   30  H12 UNL     1      -1.850   1.438  -0.251  1.00  0.00           H  
HETATM   31  H13 UNL     1      -3.324   2.157   1.141  1.00  0.00           H  
CONECT    1    2   19   20   21
CONECT    2    3   17   22
CONECT    3    4
CONECT    4    5   15   23
CONECT    5    6   14
CONECT    6    7    7   24
CONECT    7    8
CONECT    8    9    9   14
CONECT    9   10   11
CONECT   10   25   26
CONECT   11   12   12
CONECT   12   13   27
CONECT   13   14   14
CONECT   15   16   17   28
CONECT   16   29
CONECT   17   18   30
CONECT   18   31
END

HMDB0001983
     RDKit          3D
5'-Deoxyadenosine
 31 33  0  0  0  0  0  0  0  0999 V2000
   -3.5821   -0.2285   -1.5338 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6570   -0.5382   -0.3915 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.4046   -0.9559   -0.8088 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6726   -1.0021    0.3807 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7502   -0.9763    0.1435 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.5572   -2.0691    0.0983 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8109   -1.6467   -0.1429 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.8099   -0.3087   -0.2507 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7953    0.6347   -0.4896 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1332    0.1912   -0.6750 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.4548    1.9282   -0.5376 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1908    2.3382   -0.3618 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2280    1.4290   -0.1294 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.5209    0.1051   -0.0710 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1603    0.1063    1.2534 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.7892   -0.4122    2.4092 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3046    0.6907    0.4145 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.3360    1.1482    1.1901 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1629    0.4693   -2.2747 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5169    0.1831   -1.0946 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8760   -1.2098   -1.9826 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1014   -1.3272    0.2189 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9421   -1.9920    0.8513 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2107   -3.0957    0.2384 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3157   -0.3939   -1.5333 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8559    0.4505    0.0173 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9941    3.3989   -0.4148 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4190    0.8599    1.5089 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5289   -1.3720    2.5030 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8497    1.4379   -0.2510 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3239    2.1571    1.1406 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
 15 17  1  0
 17 18  1  0
 17  2  1  0
 14  5  1  0
 14  8  1  0
  1 19  1  0
  1 20  1  0
  1 21  1  0
  2 22  1  1
  4 23  1  1
  6 24  1  0
 10 25  1  0
 10 26  1  0
 12 27  1  0
 15 28  1  1
 16 29  1  0
 17 30  1  6
 18 31  1  0
M  END

Synonyms

Value	Source
5'-Deoxy-adenosine	HMDB
5'-DAdo nucleoside	MeSH, HMDB

Molecular Formula

C₁₀H₁₃N₅O₃

Average Mass

251.2419

Monoisotopic Mass

251.101839307

IUPAC Name

(2R,3R,4S,5R)-2-(6-amino-9H-purin-9-yl)-5-methyloxolane-3,4-diol

Traditional Name

5'-deoxyadenosine

CAS Registry Number

4754-39-6

SMILES

C[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C=NC2=C(N)N=CN=C12

InChI Identifier

InChI=1S/C10H13N5O3/c1-4-6(16)7(17)10(18-4)15-3-14-5-8(11)12-2-13-9(5)15/h2-4,6-7,10,16-17H,1H3,(H2,11,12,13)/t4-,6-,7-,10-/m1/s1

InChI Key

XGYIMTFOTBMPFP-KQYNXXCUSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 5'-deoxyribonucleosides. These are nucleosides in which the oxygen atom at the 5'position of the ribose moiety has been replaced by another atom. The nucleobases here are limited to purine, pyrimidine, and pyridine derivatives.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

5'-deoxyribonucleosides

Sub Class

Not Available

Direct Parent

5'-deoxyribonucleosides

Alternative Parents

Substituents

5'-deoxyribonucleoside
Glycosyl compound
N-glycosyl compound
6-aminopurine
Purine
Imidazopyrimidine
Aminopyrimidine
Imidolactam
Pyrimidine
N-substituted imidazole
Azole
Heteroaromatic compound
Imidazole
Tetrahydrofuran
1,2-diol
Secondary alcohol
Oxacycle
Azacycle
Organoheterocyclic compound
Alcohol
Organic oxygen compound
Organic nitrogen compound
Hydrocarbon derivative
Organopnictogen compound
Amine
Primary amine
Organooxygen compound
Organonitrogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

adenosines (CHEBI:17319 )
5'-deoxyribonucleoside (CHEBI:17319 )

Functional Ontology

Not Available

Physical Properties

State

Solid

Predicted Properties

Property	Value	Source
Water Solubility	9.88 g/L	ALOGPS
logP	-0.52	ALOGPS
logP	-1	ChemAxon
logS	-1.4	ALOGPS
pKa (Strongest Acidic)	12.48	ChemAxon
pKa (Strongest Basic)	3.92	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	119.31 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	61.65 m³·mol⁻¹	ChemAxon
Polarizability	24.3 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

Chromatographic Retention Times and Retention Indices

Retention Times

Not Available

Retention Indices

Not Available

Chromatographic Retention Times and Retention Indices

Retention Times

Not Available

Retention Indices

Not Available

Biological Properties

Cellular Locations

Extracellular

Biospecimen Locations

Blood
Feces
Urine

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species
MMDBp0193195	Lipoyl synthase, mitochondrial	Unknown	O43766	Homo_sapiens

Human Pathways

Pathways

Name	SMPDB/PathBank

Microbial Pathways

Pathways

Not Available

Metabolic Reactions

Reactions

This table shows at most 20 reactions. For the full list of associated reactions:

See All Associated Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria	Proteobacteria	461	Human feces; Human sputum; Human unknown; Pig ; Human ; Human pleural fluid plaque; Human dental plaque; Human nasal swab; Human feces; pleural fluid plaque; bal; Cattle ; River trout ; Chicken ; Rat ; Turkey ; Dog	Unknown; Metabolic reconstruction
Bacteria	Firmicutes	276	Human feces; Human ; Cattle ; Pig ; Catfish	Metabolic reconstruction
Bacteria	Bacteroidetes	99	Human feces; Human	Metabolic reconstruction
Bacteria	Actinobacteria	73	Human ; Human feces; Cattle	Metabolic reconstruction
Bacteria	Verrucomicrobia	1	Human ; Human feces	Metabolic reconstruction
Bacteria	Spirochaetes	6	Human feces; Human	Metabolic reconstruction
Archaea	Thaumarchaeota	1	Human feces	Metabolic reconstruction
Bacteria	Fusobacteria	19	Human feces; Human	Metabolic reconstruction
Bacteria	Synergistetes	1	Human feces	Metabolic reconstruction
Archaea	Euryarchaeota	5	Human feces; Cattle ; Human	Metabolic reconstruction
Bacteria	Planctomycetes	2	Human feces	Metabolic reconstruction
Bacteria	Thermotogae	5
Bacteria/NULL	Proteobacteria	2	Human feces; Human sputum; Human unknown; Pig ; Human ; Human pleural fluid plaque; Human dental plaque; Human nasal swab; Human feces; pleural fluid plaque; bal; Cattle ; River trout ; Chicken ; Rat ; Turkey ; Dog	Unknown; Metabolic reconstruction
Archaea/Archaea	Euryarchaeota	29	Human feces; Cattle ; Human	Metabolic reconstruction
Bacteria	Aquificae	1
Bacteria	nah	2
Bacteria	Cyanobacteria	35	Human
Bacteria	Chlorobi	9
Bacteria	Chloroflexi	3
Bacteria	Deinococcus-Thermus	4
Archaea/Archaea	Crenarchaeota	8	Human feces
Bacteria	Acidobacteria	1
Bacteria	Nitrospirae	1
Archaea	Crenarchaeota	1	Human feces
Eukaryota/Fungi	Ascomycota	1	Human feces	Unknown

Exposure Sources

Food Exposures

Other Exposures

Source Type	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Min	Max	Age	Sex	Health Condition	Data Source	Reference
Human Feces	Detected but not Quantified							HMDB
Human	Detected and Quantified	0.078	0.054	0.102	Adult (>18 years old)	Both	Normal	HMDB	15116424
Human	Detected but not Quantified							HMDB

External Links

HMDB ID

HMDB0001983

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB022781

KNApSAcK ID

Not Available

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

439182

PDB ID

Not Available

ChEBI ID

17319

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

Lee SH, Jung BH, Kim SY, Chung BC: A rapid and sensitive method for quantitation of nucleosides in human urine using liquid chromatography/mass spectrometry with direct urine injection. Rapid Commun Mass Spectrom. 2004;18(9):973-7. doi: 10.1002/rcm.1400. [PubMed:15116424 ]

Showing metabocard for 5'-Deoxyadenosine (MMDBc0030308)

MOL for #<Metabolite:0x00007f1241253960>

3D MOL for #<Metabolite:0x00007f1241253960>

3D SDF for #<Metabolite:0x00007f1241253960>

3D-SDF for #<Metabolite:0x00007f1241253960>

PDB for #<Metabolite:0x00007f1241253960>

3D PDB for #<Metabolite:0x00007f1241253960>

SMILES for #<Metabolite:0x00007f1241253960>

INCHI for #<Metabolite:0x00007f1241253960>

Structure for #<Metabolite:0x00007f1241253960>

3D Structure for #<Metabolite:0x00007f1241253960>