NP-MRD: Showing NP-Card for 2-Deoxyadenosine (NP0044222)

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Record Information

Version

1.0

Created at

2022-01-10 01:01:23 UTC

Updated at

2022-01-10 01:11:26 UTC

NP-MRD ID

NP0044222

Secondary Accession Numbers

None

Natural Product Identification

Common Name

2-Deoxyadenosine

Description

Deoxyadenosine, also known as dA, 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. Deoxyadenosine exists in all living species, ranging from bacteria to plants to humans. In humans, deoxyadenosine is involved in the mercaptopurine action pathway. Deoxyadenosine is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. Deoxyadenosine, with regard to humans, has been found to be associated with several diseases such as colorectal cancer and eosinophilic esophagitis; deoxyadenosine has also been linked to several inborn metabolic disorders including adenosine deaminase deficiency and adenylosuccinate lyase deficiency. It was first documented in 2015 (PMID: 25971195). Based on a literature review a significant number of articles have been published on Deoxyadenosine (PMID: 34514267) (PMID: 34552805) (PMID: 34519921) (PMID: 34516245).

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>
NP0044222

> <DATABASE_NAME>
NP-MRD

> <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

View in JSmol

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

Chemical Formula

C₁₀H₁₃N₅O₃

Average Mass

251.2419 Da

Monoisotopic Mass

251.10184 Da

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

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, simulated)	Ahselim			2022-01-10	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, experimental)	Ahselim			2022-01-10	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, experimental)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 600 MHz, H₂O, experimental)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Not Available

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 )

Physical Properties

State

Not Available

Experimental 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

Predicted Properties

Property	Value	Source
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

External Links

HMDB ID

HMDB0000101

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB 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

Good Scents ID

Not Available

References

General References

Rebollar-Ramos D, Ovalle-Magallanes B, Palacios-Espinosa JF, Macias-Rubalcava ML, Raja HA, Gonzalez-Andrade M, Mata R: alpha-Glucosidase and PTP-1B Inhibitors from Malbranchea dendritica. ACS Omega. 2021 Aug 25;6(35):22969-22981. doi: 10.1021/acsomega.1c03708. eCollection 2021 Sep 7. [PubMed:34514267 ]
Zhang BH, Chen W, Li HQ, Zhou EM, Hu WY, Duan YQ, Mohamad OA, Gao R, Li WJ: An antialgal compound produced by Streptomyces jiujiangensis JXJ 0074(T). Appl Microbiol Biotechnol. 2015 Sep;99(18):7673-83. doi: 10.1007/s00253-015-6584-3. Epub 2015 May 14. [PubMed:25971195 ]
Yong L, Leng AQ, Yang ZX, Xue Y: A Practical Method for Determination of Nine Nucleosides in Tricholoma matsutake by UPLC/MS and Quantitative Analysis of Multicomponents Using Single Marker Method. J Anal Methods Chem. 2021 Sep 11;2021:9571329. doi: 10.1155/2021/9571329. eCollection 2021. [PubMed:34552805 ]
Tan G, Fei Z, Wei R, Wu X, Xiao P: Development of a Novel Bioluminescence Pyrophosphate Assay for the High-Sensitivity Detection of Hepatitis B Virus. Appl Biochem Biotechnol. 2021 Sep 14. pii: 10.1007/s12010-021-03655-0. doi: 10.1007/s12010-021-03655-0. [PubMed:34519921 ]
Cilento ME, Reeve AB, Michailidis E, Ilina TV, Nagy E, Mitsuya H, Parniak MA, Tedbury PR, Sarafianos SG: Development of Human Immunodeficiency Virus Type 1 Resistance to 4'-Ethynyl-2-Fluoro-2'-Deoxyadenosine Starting with Wild-Type or Nucleoside Reverse Transcriptase Inhibitor-Resistant Strains. Antimicrob Agents Chemother. 2021 Nov 17;65(12):e0116721. doi: 10.1128/AAC.01167-21. Epub 2021 Sep 13. [PubMed:34516245 ]

Showing NP-Card for 2-Deoxyadenosine (NP0044222)

MOL for NP0044222 (2-Deoxyadenosine )

3D MOL for NP0044222 (2-Deoxyadenosine )

3D SDF for NP0044222 (2-Deoxyadenosine )

3D-SDF for NP0044222 (2-Deoxyadenosine )

PDB for NP0044222 (2-Deoxyadenosine )

3D PDB for NP0044222 (2-Deoxyadenosine )

SMILES for NP0044222 (2-Deoxyadenosine )

INCHI for NP0044222 (2-Deoxyadenosine )

Structure for NP0044222 (2-Deoxyadenosine )

3D Structure for NP0044222 (2-Deoxyadenosine )