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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2012-09-11 17:33:47 UTC

Update Date

2022-09-22 18:34:57 UTC

HMDB ID

HMDB0029956

Secondary Accession Numbers

HMDB29956

Metabolite Identification

Common Name

Nebularine

Description

Nebularine, also known as N-D-ribosylpurine or 1FKW, belongs to the class of organic compounds known as purine nucleosides. Purine nucleosides are compounds comprising a purine base attached to a ribosyl or deoxyribosyl moiety. Based on a literature review very few articles have been published on Nebularine.

Structure

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

HMDB0029956
     RDKit          3D
Nebularine
 30 32  0  0  0  0  0  0  0  0999 V2000
   -3.3835   -2.0871    0.1350 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0580   -0.9176   -0.5400 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4706    0.0972    0.4394 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3275   -0.4467    1.0131 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3007   -0.1430    0.1508 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9963   -0.2290    0.8173 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2239   -0.0819    2.1256 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5553   -0.2405    2.2930 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.1373   -0.4817    1.1034 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4268   -0.7162    0.6715 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6373   -0.9217   -0.6269 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.6693   -0.9175   -1.5651 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4047   -0.6905   -1.1633 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1355   -0.4753    0.1479 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5638    1.3078   -0.1950 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0331    1.5959   -1.4384 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0650    1.3397   -0.2873 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5778    2.4930    0.3397 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2223   -1.9316    0.6763 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3089   -1.1372   -1.3269 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9452   -0.4912   -1.0486 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2340    0.3365    1.2072 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3046   -0.7317   -0.7798 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4792    0.1256    2.9041 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2212   -0.7236    1.4125 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8988   -1.0932   -2.6256 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1569    1.9922    0.5796 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4458    1.0259   -2.1201 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4323    1.3702   -1.3400 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9557    2.7730    1.0788 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  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  2  0
  5 15  1  0
 15 16  1  0
 15 17  1  0
 17 18  1  0
 17  3  1  0
 14  6  1  0
 14  9  1  0
  1 19  1  0
  2 20  1  0
  2 21  1  0
  3 22  1  0
  5 23  1  0
  7 24  1  0
 10 25  1  0
 12 26  1  0
 15 27  1  0
 16 28  1  0
 17 29  1  0
 18 30  1  0
M  END


  Mrv1652305052017392D          

 18 20  0  0  0  0            999 V2000
   -1.7737    0.5775    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7737   -0.2467    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3512   -0.8241    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1862   -1.6500    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3612   -1.8975    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7829   -1.3192    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9479   -0.4942    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4529    0.1650    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9479    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3512   -0.7417    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6912   -0.2467    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6912    0.5775    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3512    1.0725    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2687    1.8975    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8662    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3713    0.1650    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8662   -0.4942    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7012   -1.3192    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  9  2  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
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 16  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 11 17  1  0  0  0  0
 12 13  1  0  0  0  0
 12 15  1  0  0  0  0
 13 14  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0029956

> <DATABASE_NAME>
hmdb

> <SMILES>
OCC1OC(C(O)C1O)N1C=NC2=C1N=CN=C2

> <INCHI_IDENTIFIER>
InChI=1S/C10H12N4O4/c15-2-6-7(16)8(17)10(18-6)14-4-13-5-1-11-3-12-9(5)14/h1,3-4,6-8,10,15-17H,2H2

> <INCHI_KEY>
MRWXACSTFXYYMV-UHFFFAOYSA-N

> <FORMULA>
C10H12N4O4

> <MOLECULAR_WEIGHT>
252.2267

> <EXACT_MASS>
252.085854892

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
30

> <JCHEM_AVERAGE_POLARIZABILITY>
23.45722326431765

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-(hydroxymethyl)-5-(9H-purin-9-yl)oxolane-3,4-diol

> <ALOGPS_LOGP>
-0.99

> <JCHEM_LOGP>
-1.8564954476666669

> <ALOGPS_LOGS>
-1.18

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.89122631141138

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.454004489721324

> <JCHEM_PKA_STRONGEST_BASIC>
2.0549145059013965

> <JCHEM_POLAR_SURFACE_AREA>
113.52000000000001

> <JCHEM_REFRACTIVITY>
58.1817

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.68e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
nebularine

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0029956
     RDKit          3D
Nebularine
 30 32  0  0  0  0  0  0  0  0999 V2000
   -3.3835   -2.0871    0.1350 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0580   -0.9176   -0.5400 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4706    0.0972    0.4394 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3275   -0.4467    1.0131 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3007   -0.1430    0.1508 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9963   -0.2290    0.8173 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2239   -0.0819    2.1256 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5553   -0.2405    2.2930 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.1373   -0.4817    1.1034 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4268   -0.7162    0.6715 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6373   -0.9217   -0.6269 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.6693   -0.9175   -1.5651 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4047   -0.6905   -1.1633 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1355   -0.4753    0.1479 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5638    1.3078   -0.1950 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0331    1.5959   -1.4384 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0650    1.3397   -0.2873 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5778    2.4930    0.3397 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2223   -1.9316    0.6763 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3089   -1.1372   -1.3269 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9452   -0.4912   -1.0486 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2340    0.3365    1.2072 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3046   -0.7317   -0.7798 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4792    0.1256    2.9041 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2212   -0.7236    1.4125 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8988   -1.0932   -2.6256 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1569    1.9922    0.5796 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4458    1.0259   -2.1201 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4323    1.3702   -1.3400 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9557    2.7730    1.0788 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  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  2  0
  5 15  1  0
 15 16  1  0
 15 17  1  0
 17 18  1  0
 17  3  1  0
 14  6  1  0
 14  9  1  0
  1 19  1  0
  2 20  1  0
  2 21  1  0
  3 22  1  0
  5 23  1  0
  7 24  1  0
 10 25  1  0
 12 26  1  0
 15 27  1  0
 16 28  1  0
 17 29  1  0
 18 30  1  0
M  END

HEADER    PROTEIN                                 05-MAY-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   05-MAY-20         0                                  
HETATM    1  N   UNK     0      -3.311   1.078   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0      -3.311  -0.461   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -4.389  -1.538   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0      -4.081  -3.080   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0      -2.541  -3.542   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0      -1.461  -2.463   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0      -1.769  -0.923   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0      -0.845   0.308   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0      -1.769   1.540   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       4.389  -1.385   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       3.157  -0.461   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       3.157   1.078   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       4.389   2.002   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       4.235   3.542   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       1.617   1.540   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       0.693   0.308   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       1.617  -0.923   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       1.309  -2.463   0.000  0.00  0.00           O+0
CONECT    1    2    9                                                       
CONECT    2    1    3    7                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    2    6    8                                                  
CONECT    8    7    9   16                                                  
CONECT    9    1    8                                                       
CONECT   10   11                                                            
CONECT   11   10   12   17                                                  
CONECT   12   11   13   15                                                  
CONECT   13   12   14                                                       
CONECT   14   13                                                            
CONECT   15   12   16                                                       
CONECT   16    8   15   17                                                  
CONECT   17   11   16   18                                                  
CONECT   18   17                                                            
MASTER        0    0    0    0    0    0    0    0   18    0   40    0
END

COMPND    HMDB0029956
HETATM    1  O1  UNL     1      -3.384  -2.087   0.135  1.00  0.00           O  
HETATM    2  C1  UNL     1      -3.058  -0.918  -0.540  1.00  0.00           C  
HETATM    3  C2  UNL     1      -2.471   0.097   0.439  1.00  0.00           C  
HETATM    4  O2  UNL     1      -1.327  -0.447   1.013  1.00  0.00           O  
HETATM    5  C3  UNL     1      -0.301  -0.143   0.151  1.00  0.00           C  
HETATM    6  N1  UNL     1       0.996  -0.229   0.817  1.00  0.00           N  
HETATM    7  C4  UNL     1       1.224  -0.082   2.126  1.00  0.00           C  
HETATM    8  N2  UNL     1       2.555  -0.240   2.293  1.00  0.00           N  
HETATM    9  C5  UNL     1       3.137  -0.482   1.103  1.00  0.00           C  
HETATM   10  C6  UNL     1       4.427  -0.716   0.672  1.00  0.00           C  
HETATM   11  N3  UNL     1       4.637  -0.922  -0.627  1.00  0.00           N  
HETATM   12  C7  UNL     1       3.669  -0.918  -1.565  1.00  0.00           C  
HETATM   13  N4  UNL     1       2.405  -0.691  -1.163  1.00  0.00           N  
HETATM   14  C8  UNL     1       2.136  -0.475   0.148  1.00  0.00           C  
HETATM   15  C9  UNL     1      -0.564   1.308  -0.195  1.00  0.00           C  
HETATM   16  O3  UNL     1      -0.033   1.596  -1.438  1.00  0.00           O  
HETATM   17  C10 UNL     1      -2.065   1.340  -0.287  1.00  0.00           C  
HETATM   18  O4  UNL     1      -2.578   2.493   0.340  1.00  0.00           O  
HETATM   19  H1  UNL     1      -4.222  -1.932   0.676  1.00  0.00           H  
HETATM   20  H2  UNL     1      -2.309  -1.137  -1.327  1.00  0.00           H  
HETATM   21  H3  UNL     1      -3.945  -0.491  -1.049  1.00  0.00           H  
HETATM   22  H4  UNL     1      -3.234   0.336   1.207  1.00  0.00           H  
HETATM   23  H5  UNL     1      -0.305  -0.732  -0.780  1.00  0.00           H  
HETATM   24  H6  UNL     1       0.479   0.126   2.904  1.00  0.00           H  
HETATM   25  H7  UNL     1       5.221  -0.724   1.413  1.00  0.00           H  
HETATM   26  H8  UNL     1       3.899  -1.093  -2.626  1.00  0.00           H  
HETATM   27  H9  UNL     1      -0.157   1.992   0.580  1.00  0.00           H  
HETATM   28  H10 UNL     1      -0.446   1.026  -2.120  1.00  0.00           H  
HETATM   29  H11 UNL     1      -2.432   1.370  -1.340  1.00  0.00           H  
HETATM   30  H12 UNL     1      -1.956   2.773   1.079  1.00  0.00           H  
CONECT    1    2   19
CONECT    2    3   20   21
CONECT    3    4   17   22
CONECT    4    5
CONECT    5    6   15   23
CONECT    6    7   14
CONECT    7    8    8   24
CONECT    8    9
CONECT    9   10   10   14
CONECT   10   11   25
CONECT   11   12   12
CONECT   12   13   26
CONECT   13   14   14
CONECT   15   16   17   27
CONECT   16   28
CONECT   17   18   29
CONECT   18   30
END

HMDB0029956
     RDKit          3D
Nebularine
 30 32  0  0  0  0  0  0  0  0999 V2000
   -3.3835   -2.0871    0.1350 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0580   -0.9176   -0.5400 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4706    0.0972    0.4394 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3275   -0.4467    1.0131 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3007   -0.1430    0.1508 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9963   -0.2290    0.8173 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2239   -0.0819    2.1256 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5553   -0.2405    2.2930 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.1373   -0.4817    1.1034 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4268   -0.7162    0.6715 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6373   -0.9217   -0.6269 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.6693   -0.9175   -1.5651 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4047   -0.6905   -1.1633 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1355   -0.4753    0.1479 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5638    1.3078   -0.1950 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0331    1.5959   -1.4384 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0650    1.3397   -0.2873 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5778    2.4930    0.3397 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2223   -1.9316    0.6763 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3089   -1.1372   -1.3269 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9452   -0.4912   -1.0486 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2340    0.3365    1.2072 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3046   -0.7317   -0.7798 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4792    0.1256    2.9041 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2212   -0.7236    1.4125 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8988   -1.0932   -2.6256 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1569    1.9922    0.5796 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4458    1.0259   -2.1201 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4323    1.3702   -1.3400 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9557    2.7730    1.0788 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  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  2  0
  5 15  1  0
 15 16  1  0
 15 17  1  0
 17 18  1  0
 17  3  1  0
 14  6  1  0
 14  9  1  0
  1 19  1  0
  2 20  1  0
  2 21  1  0
  3 22  1  0
  5 23  1  0
  7 24  1  0
 10 25  1  0
 12 26  1  0
 15 27  1  0
 16 28  1  0
 17 29  1  0
 18 30  1  0
M  END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
1FKW	HMDB
3-Deazaadenosine	HMDB
9-(beta -D-Ribofuranosyl)purine	HMDB
9-(beta-D-Ribofuranosyl)-9H-purine	HMDB
9-(beta-D-Ribofuranosyl)purine	HMDB
9-b-D-Ribofuranosyl-9H-purine, 9ci, 8ci	HMDB
9-beta -Ribofuranosylpurine	HMDB
9-beta-D-Ribofuranosyl-9H-purine	HMDB
9-beta-Ribofuranosylpurine	HMDB
9-Purine ribonucleoside	HMDB
9beta-D-Ribofuranosyl-9H-purine	HMDB
N-D-Ribosylpurine	HMDB
Nebularin (e)	HMDB
Nebularin e)	HMDB
Nebularin(e)	HMDB
PUR	HMDB
Purine nucleoside	HMDB
Purine ribonucleoside	HMDB
Purine riboside	HMDB
Purine-1-D-ribofuranoside	HMDB
Purine-9-beta-D-ribofuranoside	HMDB
Purinosine	HMDB
Ribosyl-isopurine	HMDB
Ribosyl-purine	HMDB
Ribosylpurine	HMDB
Nebularine	MeSH

Chemical Formula

C₁₀H₁₂N₄O₄

Average Molecular Weight

252.2267

Monoisotopic Molecular Weight

252.085854892

IUPAC Name

2-(hydroxymethyl)-5-(9H-purin-9-yl)oxolane-3,4-diol

Traditional Name

nebularine

CAS Registry Number

550-33-4

SMILES

OCC1OC(C(O)C1O)N1C=NC2=C1N=CN=C2

InChI Identifier

InChI=1S/C10H12N4O4/c15-2-6-7(16)8(17)10(18-6)14-4-13-5-1-11-3-12-9(5)14/h1,3-4,6-8,10,15-17H,2H2

InChI Key

MRWXACSTFXYYMV-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as purine nucleosides. Purine nucleosides are compounds comprising a purine base attached to a ribosyl or deoxyribosyl moiety.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Purine nucleosides

Sub Class

Not Available

Direct Parent

Purine nucleosides

Alternative Parents

Substituents

Purine nucleoside
Glycosyl compound
N-glycosyl compound
Pentose monosaccharide
Imidazopyrimidine
Purine
Monosaccharide
N-substituted imidazole
Pyrimidine
Heteroaromatic compound
Azole
Imidazole
Tetrahydrofuran
Secondary alcohol
Organoheterocyclic compound
Azacycle
Oxacycle
Primary alcohol
Organopnictogen compound
Organooxygen compound
Organonitrogen compound
Alcohol
Organic oxygen compound
Hydrocarbon derivative
Organic nitrogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Extracellular (HMDB: HMDB0029956)
Cytoplasm (HMDB: HMDB0029956)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0029956)

Source

Exogenous

Exogenous (HMDB: HMDB0029956)

Food

Food (HMDB: HMDB0029956)

Vegetable

Mushroom

Endogenous

Endogenous (HMDB: HMDB0029956)

Plant

Plant (HMDB: HMDB0029956)

Process

Not Available

Role

Not Available

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	182 - 183 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	100 mg/mL	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	16.8 g/L	ALOGPS
logP	-0.99	ALOGPS
logP	-1.9	ChemAxon
logS	-1.2	ALOGPS
pKa (Strongest Acidic)	12.45	ChemAxon
pKa (Strongest Basic)	2.05	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	113.52 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	58.18 m³·mol⁻¹	ChemAxon
Polarizability	23.46 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
DarkChem	[M+H]+	156.279	31661259
DarkChem	[M-H]-	155.458	31661259
DeepCCS	[M+H]+	150.06	30932474
DeepCCS	[M-H]-	147.702	30932474
DeepCCS	[M-2H]-	180.738	30932474
DeepCCS	[M+Na]+	156.154	30932474
AllCCS	[M+H]+	157.9	32859911
AllCCS	[M+H-H2O]+	154.1	32859911
AllCCS	[M+NH4]+	161.4	32859911
AllCCS	[M+Na]+	162.4	32859911
AllCCS	[M-H]-	156.1	32859911
AllCCS	[M+Na-2H]-	155.7	32859911
AllCCS	[M+HCOO]-	155.3	32859911

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.	1.87 minutes	32390414
Predicted by Siyang on May 30, 2022	9.4087 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	3.34 minutes	32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid	193.7 seconds	40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	1241.3 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	258.3 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	70.1 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	161.9 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	64.1 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	322.1 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	263.5 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	524.8 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	599.3 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	82.8 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	882.3 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	181.1 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	177.1 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	528.1 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	342.6 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	230.0 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Nebularine	OCC1OC(C(O)C1O)N1C=NC2=C1N=CN=C2	3259.7	Standard polar	33892256
Nebularine	OCC1OC(C(O)C1O)N1C=NC2=C1N=CN=C2	1944.0	Standard non polar	33892256
Nebularine	OCC1OC(C(O)C1O)N1C=NC2=C1N=CN=C2	2454.3	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Nebularine,1TMS,isomer #1	C[Si](C)(C)OCC1OC(N2C=NC3=CN=CN=C32)C(O)C1O	2438.1	Semi standard non polar	33892256
Nebularine,1TMS,isomer #2	C[Si](C)(C)OC1C(O)C(CO)OC1N1C=NC2=CN=CN=C21	2449.4	Semi standard non polar	33892256
Nebularine,1TMS,isomer #3	C[Si](C)(C)OC1C(CO)OC(N2C=NC3=CN=CN=C32)C1O	2461.3	Semi standard non polar	33892256
Nebularine,2TMS,isomer #1	C[Si](C)(C)OCC1OC(N2C=NC3=CN=CN=C32)C(O[Si](C)(C)C)C1O	2394.3	Semi standard non polar	33892256
Nebularine,2TMS,isomer #2	C[Si](C)(C)OCC1OC(N2C=NC3=CN=CN=C32)C(O)C1O[Si](C)(C)C	2413.3	Semi standard non polar	33892256
Nebularine,2TMS,isomer #3	C[Si](C)(C)OC1C(CO)OC(N2C=NC3=CN=CN=C32)C1O[Si](C)(C)C	2396.6	Semi standard non polar	33892256
Nebularine,3TMS,isomer #1	C[Si](C)(C)OCC1OC(N2C=NC3=CN=CN=C32)C(O[Si](C)(C)C)C1O[Si](C)(C)C	2387.9	Semi standard non polar	33892256
Nebularine,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCC1OC(N2C=NC3=CN=CN=C32)C(O)C1O	2663.7	Semi standard non polar	33892256
Nebularine,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC1C(O)C(CO)OC1N1C=NC2=CN=CN=C21	2664.9	Semi standard non polar	33892256
Nebularine,1TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OC1C(CO)OC(N2C=NC3=CN=CN=C32)C1O	2674.2	Semi standard non polar	33892256
Nebularine,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCC1OC(N2C=NC3=CN=CN=C32)C(O[Si](C)(C)C(C)(C)C)C1O	2831.8	Semi standard non polar	33892256
Nebularine,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OCC1OC(N2C=NC3=CN=CN=C32)C(O)C1O[Si](C)(C)C(C)(C)C	2846.7	Semi standard non polar	33892256
Nebularine,2TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OC1C(CO)OC(N2C=NC3=CN=CN=C32)C1O[Si](C)(C)C(C)(C)C	2848.7	Semi standard non polar	33892256
Nebularine,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCC1OC(N2C=NC3=CN=CN=C32)C(O[Si](C)(C)C(C)(C)C)C1O[Si](C)(C)C(C)(C)C	3006.1	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Nebularine GC-MS (Non-derivatized) - 70eV, Positive	splash10-05c6-9320000000-8568cb65887589a7c24c	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Nebularine GC-MS (3 TMS) - 70eV, Positive	splash10-0umr-6549300000-2f2e367dec1b5b795a90	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Nebularine GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Experimental LC-MS/MS	LC-MS/MS Spectrum - Nebularine LC-ESI-QTOF , positive-QTOF	splash10-0079-0900000000-56dbcaa78636ebb05d35	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Nebularine LC-ESI-QTOF , positive-QTOF	splash10-0079-0900000000-88d4f77072df7340a924	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Nebularine LC-ESI-QTOF , positive-QTOF	splash10-00y0-0900000000-e3a077bcd64184c0deba	2017-09-14	HMDB team, MONA	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Nebularine 10V, Positive-QTOF	splash10-00di-0940000000-558c13580fe37e7be7cc	2015-04-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Nebularine 20V, Positive-QTOF	splash10-00di-2900000000-15f6248a2b75854f25d7	2015-04-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Nebularine 40V, Positive-QTOF	splash10-00dl-9800000000-6bd857bf607d73c94c21	2015-04-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Nebularine 10V, Negative-QTOF	splash10-0uxr-0790000000-52cdec17cf806f6a8d60	2015-04-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Nebularine 20V, Negative-QTOF	splash10-014i-1900000000-28abc2355f386333f114	2015-04-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Nebularine 40V, Negative-QTOF	splash10-00kf-9600000000-fb33005da35ddacd66d1	2015-04-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Nebularine 10V, Negative-QTOF	splash10-0ue9-1490000000-6dc9f80c37f021faecb5	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Nebularine 20V, Negative-QTOF	splash10-014i-3900000000-b5dcc04009267c01b343	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Nebularine 40V, Negative-QTOF	splash10-014i-3900000000-f19c5dbdfad54ebaea77	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Nebularine 10V, Positive-QTOF	splash10-00di-1920000000-fa2d03f63315e3200123	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Nebularine 20V, Positive-QTOF	splash10-00di-1910000000-7e964acf962463d5cccc	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Nebularine 40V, Positive-QTOF	splash10-00dl-4900000000-23f6f050c47dd1bef673	2021-09-24	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm
Extracellular

Biospecimen Locations

Blood
Urine

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	34436864	details
Urine	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	34436864	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

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

248425

PDB ID

Not Available

ChEBI ID

139743

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1812481

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

(). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .

Enzymes

Enzyme Details

1. Adenosine deaminase

General function:: Involved in deaminase activity
Specific function:: Catalyzes the hydrolytic deamination of adenosine and 2-deoxyadenosine. Plays an important role in purine metabolism and in adenosine homeostasis. Modulates signaling by extracellular adenosine, and so contributes indirectly to cellular signaling events. Acts as a positive regulator of T-cell coactivation, by binding DPP4. Its interaction with DPP4 regulates lymphocyte-epithelial cell adhesion.
Gene Name:: ADA
Uniprot ID:: P00813
Molecular weight:: 40764.13

References

Overington JP, Al-Lazikani B, Hopkins AL: How many drug targets are there? Nat Rev Drug Discov. 2006 Dec;5(12):993-6. [PubMed:17139284 ]
Imming P, Sinning C, Meyer A: Drugs, their targets and the nature and number of drug targets. Nat Rev Drug Discov. 2006 Oct;5(10):821-34. [PubMed:17016423 ]
Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE: The Protein Data Bank. Nucleic Acids Res. 2000 Jan 1;28(1):235-42. [PubMed:10592235 ]

Enzyme Details

2. Purine nucleoside phosphorylase

General function:: Involved in purine-nucleoside phosphorylase activity
Specific function:: The purine nucleoside phosphorylases catalyze the phosphorolytic breakdown of the N-glycosidic bond in the beta-(deoxy)ribonucleoside molecules, with the formation of the corresponding free purine bases and pentose-1-phosphate.
Gene Name:: PNP
Uniprot ID:: P00491
Molecular weight:: 32117.69

Reactions

Nebularine + Phosphate → Purine + Ribose 1-phosphate	details

Showing metabocard for Nebularine (HMDB0029956)

MOL for HMDB0029956 (Nebularine)

3D MOL for HMDB0029956 (Nebularine)

3D SDF for HMDB0029956 (Nebularine)

3D-SDF for HMDB0029956 (Nebularine)

PDB for HMDB0029956 (Nebularine)

3D PDB for HMDB0029956 (Nebularine)

SMILES for HMDB0029956 (Nebularine)

INCHI for HMDB0029956 (Nebularine)

Structure for HMDB0029956 (Nebularine)

3D Structure for HMDB0029956 (Nebularine)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

Enzymes

References

Reactions