NP-MRD: Showing NP-Card for Deoxyguanosine (NP0001241)

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Record Information

Version

2.0

Created at

2005-11-16 15:48:42 UTC

Updated at

2022-01-10 00:21:46 UTC

NP-MRD ID

NP0001241

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Deoxyguanosine

Description

Deoxyguanosine, also known as dG, 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’. Deoxyguanosine is a nucleoside consisting of the base guanine and the sugar deoxyribose. Deoxyguanosine is one of the four deoxyribonucleosides that make up DNA. Deoxyguanosine exists in all living species, ranging from bacteria to plants to humans. Deoxyguanosine participates in a number of enzymatic reactions. In particular, deoxyguanosine can be biosynthesized from 2'-deoxyguanosine 5'-monophosphate through the enzyme known as cytosolic purine 5'-nucleotidase. In addition, deoxyguanosine can be converted into 2'-deoxyguanosine 5'-monophosphate (dGMP); which is mediated by the enzyme deoxyguanosine kinase. Deoxyguanosine is involved in the rare, inherited metabolic disorder called the purine nucleoside phosphorylase deficiency (PNP deficiency). In particular PNP deficiency is characterized by elevated levels of dGTP (deoxyguanosine triphosphate). PNP accounts for approximately 4% of patients with severe combined immunodeficiency (PMID: 1931007 ). PNP-deficient patients suffer from recurrent infections, usually beginning in the first year of life. Two thirds of patients have evidence of neurologic disorders with spasticity, developmental delay and mental retardation. Deoxyguanosine can be converted to 8-hydroxy-deoxyguanosine (8-OHdG) due to hydroxyl radical attack at the C8 of guanine. 8-Hydroxy-deoxyguanosine is a sensitive marker of the DNA damage This damage, if left unrepaired, has been proposed to contribute to mutagenicity and cancer promotion.

Structure

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

HMDB0000085
     RDKit          3D
Deoxyguanosine
 32 34  0  0  0  0  0  0  0  0999 V2000
    4.3718   -2.0550    0.1038 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.7318   -0.7937   -0.1007 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3868   -0.7145    0.0077 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7010    0.4263   -0.1673 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4404    1.5703   -0.4754 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5235    2.5474   -0.5946 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.2803    2.0653   -0.3781 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3967    0.7565   -0.1151 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6539   -0.1493    0.1722 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.5848    0.3511    1.2776 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6364   -0.7341    1.1595 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.0805   -1.9032    1.6717 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6945   -0.8801   -0.3473 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.9512   -0.1232   -0.7989 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9057    1.1988   -0.3888 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5584   -0.3210   -0.8687 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8136    1.4809   -0.5843 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4676    2.5032   -0.8591 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4464    0.3027   -0.3966 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.3796   -2.4398    1.0734 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8209   -2.5899   -0.6701 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6341    2.6754   -0.4207 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3128   -1.1507    0.5042 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0865    0.3505    2.2592 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0154    1.3033    0.9811 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5908   -0.4657    1.6079 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7634   -2.5168    0.9448 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7903   -1.9306   -0.6606 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8531   -0.5891   -0.3705 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0151   -0.2003   -1.9042 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1274    1.7723   -1.1783 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4938    0.2529   -0.4835 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  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 11 13  1  0
 13 14  1  0
 14 15  1  0
 13 16  1  0
  5 17  1  0
 17 18  2  0
 17 19  1  0
 19  2  1  0
  8  4  1  0
 16  9  1  0
  1 20  1  0
  1 21  1  0
  7 22  1  0
  9 23  1  1
 10 24  1  0
 10 25  1  0
 11 26  1  1
 12 27  1  0
 13 28  1  1
 14 29  1  0
 14 30  1  0
 15 31  1  0
 19 32  1  0
M  END


  Mrv1652309032023512D          

 19 21  0  0  0  0            999 V2000
    4.9452    0.3673    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2308   -0.0451    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.9452   -1.2827    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.6597   -0.8702    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6597   -0.0451    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4443    0.2096    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.9293   -0.4578    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4443   -1.1252    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.6993   -1.9100    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.2143   -2.5773    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.6992   -3.2449    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.4442   -4.0295    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9963   -4.6426    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.4838   -2.9899    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    8.1513   -3.4749    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.4839   -2.1649    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2307   -0.8702    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5162   -1.2827    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.9452    1.1923    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 19  1  2  0  0  0  0
  1  2  1  0  0  0  0
  1  5  1  0  0  0  0
  2 17  1  0  0  0  0
 17  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  4  8  1  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
  9  8  1  1  0  0  0
  9 10  1  0  0  0  0
  9 16  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  1  0  0  0
 11 14  1  0  0  0  0
 12 13  1  0  0  0  0
 14 15  1  6  0  0  0
 14 16  1  0  0  0  0
 17 18  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0001241

> <DATABASE_NAME>
NP-MRD

> <SMILES>
NC1=NC2=C(N=CN2[C@H]2C[C@H](O)[C@@H](CO)O2)C(=O)N1

> <INCHI_IDENTIFIER>
InChI=1S/C10H13N5O4/c11-10-13-8-7(9(18)14-10)12-3-15(8)6-1-4(17)5(2-16)19-6/h3-6,16-17H,1-2H2,(H3,11,13,14,18)/t4-,5+,6+/m0/s1

> <INCHI_KEY>
YKBGVTZYEHREMT-KVQBGUIXSA-N

> <FORMULA>
C10H13N5O4

> <MOLECULAR_WEIGHT>
267.2413

> <EXACT_MASS>
267.096753929

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
32

> <JCHEM_AVERAGE_POLARIZABILITY>
25.238180518018385

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-amino-9-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-6,9-dihydro-1H-purin-6-one

> <ALOGPS_LOGP>
-1.75

> <JCHEM_LOGP>
-1.8055801330000003

> <ALOGPS_LOGS>
-1.37

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.886841415564113

> <JCHEM_PKA_STRONGEST_ACIDIC>
10.158527534112794

> <JCHEM_PKA_STRONGEST_BASIC>
0.4648935108305678

> <JCHEM_POLAR_SURFACE_AREA>
134.98999999999998

> <JCHEM_REFRACTIVITY>
63.110399999999984

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.15e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-deoxyguanosine

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0000085
     RDKit          3D
Deoxyguanosine
 32 34  0  0  0  0  0  0  0  0999 V2000
    4.3718   -2.0550    0.1038 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.7318   -0.7937   -0.1007 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3868   -0.7145    0.0077 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7010    0.4263   -0.1673 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4404    1.5703   -0.4754 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5235    2.5474   -0.5946 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.2803    2.0653   -0.3781 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3967    0.7565   -0.1151 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6539   -0.1493    0.1722 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.5848    0.3511    1.2776 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6364   -0.7341    1.1595 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.0805   -1.9032    1.6717 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6945   -0.8801   -0.3473 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.9512   -0.1232   -0.7989 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9057    1.1988   -0.3888 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5584   -0.3210   -0.8687 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8136    1.4809   -0.5843 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4676    2.5032   -0.8591 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4464    0.3027   -0.3966 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.3796   -2.4398    1.0734 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8209   -2.5899   -0.6701 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6341    2.6754   -0.4207 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3128   -1.1507    0.5042 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0865    0.3505    2.2592 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0154    1.3033    0.9811 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5908   -0.4657    1.6079 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7634   -2.5168    0.9448 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7903   -1.9306   -0.6606 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8531   -0.5891   -0.3705 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0151   -0.2003   -1.9042 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1274    1.7723   -1.1783 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4938    0.2529   -0.4835 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  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 11 13  1  0
 13 14  1  0
 14 15  1  0
 13 16  1  0
  5 17  1  0
 17 18  2  0
 17 19  1  0
 19  2  1  0
  8  4  1  0
 16  9  1  0
  1 20  1  0
  1 21  1  0
  7 22  1  0
  9 23  1  1
 10 24  1  0
 10 25  1  0
 11 26  1  1
 12 27  1  0
 13 28  1  1
 14 29  1  0
 14 30  1  0
 15 31  1  0
 19 32  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  C   UNK     0       9.231   0.686   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0       7.897  -0.084   0.000  0.00  0.00           N+0
HETATM    3  N   UNK     0       9.231  -2.394   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0      10.565  -1.624   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      10.565  -0.084   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0      12.029   0.391   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0      12.935  -0.855   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0      12.029  -2.100   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0      12.505  -3.565   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      11.600  -4.811   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0      12.505  -6.057   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      12.029  -7.522   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      13.060  -8.666   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0      13.970  -5.581   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      15.216  -6.486   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      13.970  -4.041   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       7.897  -1.624   0.000  0.00  0.00           C+0
HETATM   18  N   UNK     0       6.564  -2.394   0.000  0.00  0.00           N+0
HETATM   19  O   UNK     0       9.231   2.226   0.000  0.00  0.00           O+0
CONECT    1   19    2    5                                                  
CONECT    2    1   17                                                       
CONECT    3   17    4                                                       
CONECT    4    3    5    8                                                  
CONECT    5    1    4    6                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    4    7    9                                                  
CONECT    9    8   10   16                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12   14                                                  
CONECT   12   11   13                                                       
CONECT   13   12                                                            
CONECT   14   11   15   16                                                  
CONECT   15   14                                                            
CONECT   16    9   14                                                       
CONECT   17    2    3   18                                                  
CONECT   18   17                                                            
CONECT   19    1                                                            
MASTER        0    0    0    0    0    0    0    0   19    0   42    0
END

COMPND    HMDB0000085
HETATM    1  N1  UNL     1       4.372  -2.055   0.104  1.00  0.00           N  
HETATM    2  C1  UNL     1       3.732  -0.794  -0.101  1.00  0.00           C  
HETATM    3  N2  UNL     1       2.387  -0.714   0.008  1.00  0.00           N  
HETATM    4  C2  UNL     1       1.701   0.426  -0.167  1.00  0.00           C  
HETATM    5  C3  UNL     1       2.440   1.570  -0.475  1.00  0.00           C  
HETATM    6  N3  UNL     1       1.523   2.547  -0.595  1.00  0.00           N  
HETATM    7  C4  UNL     1       0.280   2.065  -0.378  1.00  0.00           C  
HETATM    8  N4  UNL     1       0.397   0.757  -0.115  1.00  0.00           N  
HETATM    9  C5  UNL     1      -0.654  -0.149   0.172  1.00  0.00           C  
HETATM   10  C6  UNL     1      -1.585   0.351   1.278  1.00  0.00           C  
HETATM   11  C7  UNL     1      -2.636  -0.734   1.160  1.00  0.00           C  
HETATM   12  O1  UNL     1      -2.081  -1.903   1.672  1.00  0.00           O  
HETATM   13  C8  UNL     1      -2.694  -0.880  -0.347  1.00  0.00           C  
HETATM   14  C9  UNL     1      -3.951  -0.123  -0.799  1.00  0.00           C  
HETATM   15  O2  UNL     1      -3.906   1.199  -0.389  1.00  0.00           O  
HETATM   16  O3  UNL     1      -1.558  -0.321  -0.869  1.00  0.00           O  
HETATM   17  C10 UNL     1       3.814   1.481  -0.584  1.00  0.00           C  
HETATM   18  O4  UNL     1       4.468   2.503  -0.859  1.00  0.00           O  
HETATM   19  N5  UNL     1       4.446   0.303  -0.397  1.00  0.00           N  
HETATM   20  H1  UNL     1       4.380  -2.440   1.073  1.00  0.00           H  
HETATM   21  H2  UNL     1       4.821  -2.590  -0.670  1.00  0.00           H  
HETATM   22  H3  UNL     1      -0.634   2.675  -0.421  1.00  0.00           H  
HETATM   23  H4  UNL     1      -0.313  -1.151   0.504  1.00  0.00           H  
HETATM   24  H5  UNL     1      -1.087   0.350   2.259  1.00  0.00           H  
HETATM   25  H6  UNL     1      -2.015   1.303   0.981  1.00  0.00           H  
HETATM   26  H7  UNL     1      -3.591  -0.466   1.608  1.00  0.00           H  
HETATM   27  H8  UNL     1      -1.763  -2.517   0.945  1.00  0.00           H  
HETATM   28  H9  UNL     1      -2.790  -1.931  -0.661  1.00  0.00           H  
HETATM   29  H10 UNL     1      -4.853  -0.589  -0.371  1.00  0.00           H  
HETATM   30  H11 UNL     1      -4.015  -0.200  -1.904  1.00  0.00           H  
HETATM   31  H12 UNL     1      -4.127   1.772  -1.178  1.00  0.00           H  
HETATM   32  H13 UNL     1       5.494   0.253  -0.484  1.00  0.00           H  
CONECT    1    2   20   21
CONECT    2    3    3   19
CONECT    3    4
CONECT    4    5    5    8
CONECT    5    6   17
CONECT    6    7    7
CONECT    7    8   22
CONECT    8    9
CONECT    9   10   16   23
CONECT   10   11   24   25
CONECT   11   12   13   26
CONECT   12   27
CONECT   13   14   16   28
CONECT   14   15   29   30
CONECT   15   31
CONECT   17   18   18   19
CONECT   19   32
END

HMDB0000085
     RDKit          3D
Deoxyguanosine
 32 34  0  0  0  0  0  0  0  0999 V2000
    4.3718   -2.0550    0.1038 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.7318   -0.7937   -0.1007 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3868   -0.7145    0.0077 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7010    0.4263   -0.1673 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4404    1.5703   -0.4754 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5235    2.5474   -0.5946 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.2803    2.0653   -0.3781 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3967    0.7565   -0.1151 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6539   -0.1493    0.1722 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.5848    0.3511    1.2776 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6364   -0.7341    1.1595 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.0805   -1.9032    1.6717 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6945   -0.8801   -0.3473 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.9512   -0.1232   -0.7989 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9057    1.1988   -0.3888 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5584   -0.3210   -0.8687 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8136    1.4809   -0.5843 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4676    2.5032   -0.8591 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4464    0.3027   -0.3966 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.3796   -2.4398    1.0734 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8209   -2.5899   -0.6701 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6341    2.6754   -0.4207 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3128   -1.1507    0.5042 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0865    0.3505    2.2592 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0154    1.3033    0.9811 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5908   -0.4657    1.6079 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7634   -2.5168    0.9448 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7903   -1.9306   -0.6606 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8531   -0.5891   -0.3705 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0151   -0.2003   -1.9042 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1274    1.7723   -1.1783 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4938    0.2529   -0.4835 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  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 11 13  1  0
 13 14  1  0
 14 15  1  0
 13 16  1  0
  5 17  1  0
 17 18  2  0
 17 19  1  0
 19  2  1  0
  8  4  1  0
 16  9  1  0
  1 20  1  0
  1 21  1  0
  7 22  1  0
  9 23  1  1
 10 24  1  0
 10 25  1  0
 11 26  1  1
 12 27  1  0
 13 28  1  1
 14 29  1  0
 14 30  1  0
 15 31  1  0
 19 32  1  0
M  END

View in JSmol

Synonyms

Value	Source
2-Amino-9-(2-deoxy-9-beta-D-ribofuranosyl)-9H-purin-6-ol	ChEBI
9-(2-Deoxy-beta-D-erythro-pentofuranosyl)-guanine	ChEBI
dG	ChEBI
Guanine deoxy nucleoside	ChEBI
2'-Deoxyguanosine	Kegg
2-Amino-9-(2-deoxy-9-b-D-ribofuranosyl)-9H-purin-6-ol	Generator
2-Amino-9-(2-deoxy-9-β-D-ribofuranosyl)-9H-purin-6-ol	Generator
9-(2-Deoxy-b-D-erythro-pentofuranosyl)-guanine	Generator
9-(2-Deoxy-β-D-erythro-pentofuranosyl)-guanine	Generator
2'-Deoxy-guanosine	HMDB
2-Deoxyguanosine	HMDB
9-(2-Deoxy-b-D-erythro-pentofuranosyl)guanine	HMDB
9-(2-Deoxy-beta-delta-erythro-pentofuranosyl)-guanine	HMDB
9-(2-Deoxy-beta-delta-erythro-pentofuranosyl)guanine	HMDB
Desoxyguanosine	HMDB
Guanine deoxyriboside	HMDB
Deoxyguanosine	ChEBI

Chemical Formula

C₁₀H₁₃N₅O₄

Average Mass

267.2413 Da

Monoisotopic Mass

267.09675 Da

IUPAC Name

2-amino-9-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-6,9-dihydro-1H-purin-6-one

Traditional Name

2-deoxyguanosine

CAS Registry Number

961-07-9

SMILES

NC1=NC2=C(N=CN2[C@H]2C[C@H](O)[C@@H](CO)O2)C(=O)N1

InChI Identifier

InChI=1S/C10H13N5O4/c11-10-13-8-7(9(18)14-10)12-3-15(8)6-1-4(17)5(2-16)19-6/h3-6,16-17H,1-2H2,(H3,11,13,14,18)/t4-,5+,6+/m0/s1

InChI Key

YKBGVTZYEHREMT-KVQBGUIXSA-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, 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

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Asterias forbesi	LOTUS Database	35616633
Cannabis sativa	CannabisDB	Not Available
Ctenodiscus crispatus	LOTUS Database	35616633
Daphnia pulex	LOTUS Database	35616633
Homo sapiens	LOTUS Database	35616633
Leptasterias polaris	LOTUS Database	35616633
Mus musculus	LOTUS Database	35616633
Phaseolus vulgaris	KNApSAcK Database	22123792

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-oxopurine
Hypoxanthine
Purinone
Imidazopyrimidine
Purine
Aminopyrimidine
Pyrimidone
N-substituted imidazole
Pyrimidine
Azole
Imidazole
Heteroaromatic compound
Vinylogous amide
Tetrahydrofuran
Secondary alcohol
Oxacycle
Azacycle
Organoheterocyclic compound
Amine
Primary amine
Primary alcohol
Organooxygen compound
Organonitrogen compound
Hydrocarbon derivative
Organic oxide
Alcohol
Organopnictogen compound
Organic nitrogen compound
Organic oxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

purine 2'-deoxyribonucleoside (CHEBI:17172 )
Deoxyribonucleosides (C00330 )

Physical Properties

State

Solid

Experimental Properties

Property	Value	Reference
Melting Point	300 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	-1.30	Balzarini, J., Matthes, E., Meeus, P., Johns, D. G. & De Clercq, E. (1988) Proceedings of the VI International Symposium on Human Purine and Pyrimidine Metabolism, Hakone, Japan, July 17-21, 1988.

Predicted Properties

Property	Value	Source
Water Solubility	11.5 g/L	ALOGPS
logP	-1.8	ALOGPS
logP	-1.8	ChemAxon
logS	-1.4	ALOGPS
pKa (Strongest Acidic)	10.16	ChemAxon
pKa (Strongest Basic)	0.46	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	134.99 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	63.11 m³·mol⁻¹	ChemAxon
Polarizability	25.24 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

HMDB0000085

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

17172

Good Scents ID

Not Available

References

General References

Gao K, Henning SM, Niu Y, Youssefian AA, Seeram NP, Xu A, Heber D: The citrus flavonoid naringenin stimulates DNA repair in prostate cancer cells. J Nutr Biochem. 2006 Feb;17(2):89-95. Epub 2005 Jun 20. [PubMed:16111881 ]
Podmore K, Farmer PB, Herbert KE, Jones GD, Martin EA: 32P-postlabelling approaches for the detection of 8-oxo-2'-deoxyguanosine-3'-monophosphate in DNA. Mutat Res. 1997 Aug 1;378(1-2):139-49. [PubMed:9288892 ]
Shibata T, Iio K, Kawai Y, Shibata N, Kawaguchi M, Toi S, Kobayashi M, Kobayashi M, Yamamoto K, Uchida K: Identification of a lipid peroxidation product as a potential trigger of the p53 pathway. J Biol Chem. 2006 Jan 13;281(2):1196-204. Epub 2005 Oct 26. [PubMed:16251187 ]
Gackowski D, Ciecierski M, Jawien A, Olinski R: Background level of 8-oxo-2'-deoxyguanosine in lymphocyte DNA does not correlate with the concentration of antioxidant vitamins in blood plasma. Acta Biochim Pol. 2001;48(2):535-9. [PubMed:11732622 ]
Takamura-Enya T, Watanabe M, Totsuka Y, Kanazawa T, Matsushima-Hibiya Y, Koyama K, Sugimura T, Wakabayashi K: Mono(ADP-ribosyl)ation of 2'-deoxyguanosine residue in DNA by an apoptosis-inducing protein, pierisin-1, from cabbage butterfly. Proc Natl Acad Sci U S A. 2001 Oct 23;98(22):12414-9. Epub 2001 Oct 9. [PubMed:11592983 ]
Palozza P, Serini S, Di Nicuolo F, Boninsegna A, Torsello A, Maggiano N, Ranelletti FO, Wolf FI, Calviello G, Cittadini A: beta-Carotene exacerbates DNA oxidative damage and modifies p53-related pathways of cell proliferation and apoptosis in cultured cells exposed to tobacco smoke condensate. Carcinogenesis. 2004 Aug;25(8):1315-25. Epub 2004 Apr 8. [PubMed:15073048 ]
Zaidi SN, Laidlaw I, Howell A, Potten CS, Cooper DP, O'Connor PJ: Normal human breast xenografts activate N-nitrosodimethylamine: identification of potential target cells for an environmental nitrosamine. Br J Cancer. 1992 Jul;66(1):79-83. [PubMed:1637681 ]
Gackowski D, Banaszkiewicz Z, Rozalski R, Jawien A, Olinski R: Persistent oxidative stress in colorectal carcinoma patients. Int J Cancer. 2002 Oct 1;101(4):395-7. [PubMed:12209966 ]
Araki S, Hayashi M, Tamagawa K, Saito M, Kato S, Komori T, Sakakihara Y, Mizutani T, Oda M: Neuropathological analysis in spinal muscular atrophy type II. Acta Neuropathol. 2003 Nov;106(5):441-8. Epub 2003 Jul 25. [PubMed:12898156 ]
Kato I, Ren J, Heilbrun LK, Djuric Z: Intra- and inter-individual variability in measurements of biomarkers for oxidative damage in vivo: Nutrition and Breast Health Study. Biomarkers. 2006 Mar-Apr;11(2):143-52. [PubMed:16766390 ]
Izzedine H, Launay-Vacher V, Aymard G, Legrand M, Deray G: Pharmacokinetics of abacavir in HIV-1-infected patients with impaired renal function. Nephron. 2001 Sep;89(1):62-7. [PubMed:11528234 ]
Bowen P, Chen L, Stacewicz-Sapuntzakis M, Duncan C, Sharifi R, Ghosh L, Kim HS, Christov-Tzelkov K, van Breemen R: Tomato sauce supplementation and prostate cancer: lycopene accumulation and modulation of biomarkers of carcinogenesis. Exp Biol Med (Maywood). 2002 Nov;227(10):886-93. [PubMed:12424330 ]
Staal GE, Stoop JW, Zegers BJ, Siegenbeek van Heukelom LH, van der Vlist MJ, Wadman SK, Martin DW: Erythrocyte metabolism in purine nucleoside phosphorylase deficiency after enzyme replacement therapy by infusion of erythrocytes. J Clin Invest. 1980 Jan;65(1):103-8. [PubMed:6765955 ]
Blair IA: Lipid hydroperoxide-mediated DNA damage. Exp Gerontol. 2001 Sep;36(9):1473-81. [PubMed:11525870 ]
Schramm VL: Development of transition state analogues of purine nucleoside phosphorylase as anti-T-cell agents. Biochim Biophys Acta. 2002 Jul 18;1587(2-3):107-17. [PubMed:12084452 ]
Schilderman PA, Rhijnsburger E, Zwingmann I, Kleinjans JC: Induction of oxidative DNA damages and enhancement of cell proliferation in human lymphocytes in vitro by butylated hydroxyanisole. Carcinogenesis. 1995 Mar;16(3):507-12. [PubMed:7697806 ]
Kaneko T, Tahara S: Formation of 8-oxo-2'-deoxyguanosine in the DNA of human diploid fibroblasts by treatment with linoleic acid hydroperoxide and ferric ion. Lipids. 2000 Sep;35(9):961-5. [PubMed:11026616 ]
Hou SM, Nori P, Fang JL, Vaca CE: Methylglyoxal induces hprt mutation and DNA adducts in human T-lymphocytes in vitro. Environ Mol Mutagen. 1995;26(4):286-91. [PubMed:8575417 ]
Bialkowski K, Kowara R, Windorbska W, Olinski R: 8-Oxo-2'-deoxyguanosine level in lymphocytes DNA of cancer patients undergoing radiotherapy. Cancer Lett. 1996 Jan 19;99(1):93-7. [PubMed:8564935 ]
Markert ML: Purine nucleoside phosphorylase deficiency. Immunodefic Rev. 1991;3(1):45-81. [PubMed:1931007 ]
Wan J, Chen R, Yang Z, Xi J, Cao Y, Chen Y, Zhang X, Luan Y: Aristolochic acid IVa forms DNA adducts in vitro but is non-genotoxic in vivo. Arch Toxicol. 2021 Aug;95(8):2839-2850. doi: 10.1007/s00204-021-03077-1. Epub 2021 Jul 5. [PubMed:34223934 ]

Showing NP-Card for Deoxyguanosine (NP0001241)

MOL for NP0001241 (Deoxyguanosine)

3D MOL for NP0001241 (Deoxyguanosine)

3D SDF for NP0001241 (Deoxyguanosine)

3D-SDF for NP0001241 (Deoxyguanosine)

PDB for NP0001241 (Deoxyguanosine)

3D PDB for NP0001241 (Deoxyguanosine)

SMILES for NP0001241 (Deoxyguanosine)

INCHI for NP0001241 (Deoxyguanosine)

Structure for NP0001241 (Deoxyguanosine)

3D Structure for NP0001241 (Deoxyguanosine)