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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-11 19:09:09 UTC

Update Date

2021-09-26 23:14:38 UTC

HMDB ID

HMDB0257989

Secondary Accession Numbers

None

Metabolite Identification

Common Name

1-[(2R,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxypyrimidin-2-one

Description

1-[(2R,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxypyrimidin-2-one belongs to the class of organic compounds known as pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms. Based on a literature review very few articles have been published on 1-[(2R,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxypyrimidin-2-one. This compound has been identified in human blood as reported by (PMID: 31557052 ). 1-[(2r,3r,4s,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxypyrimidin-2-one is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 1-[(2R,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxypyrimidin-2-one is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.

Structure

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

HMDB0257989
     RDKit          3D
1-[(2R,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxypyrimidin-2-one
 29 30  0  0  0  0  0  0  0  0999 V2000
    1.6144    1.6538   -1.7791 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5437    1.0076   -1.1872 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8152    1.4180   -1.1894 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.8072    0.7563   -0.5752 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4810   -0.4060    0.0884 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1665   -0.8055    0.0751 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1908   -0.1090   -0.5576 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.9042   -0.5367   -0.5475 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1596    0.2965   -0.1244 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1409    0.4112   -1.0693 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3590    0.3095   -0.4502 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4935   -0.0141   -1.3655 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3418   -1.2190   -2.0338 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1145   -0.7876    0.5777 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0865   -0.7601    1.5712 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7552   -0.3252    1.1107 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0344    0.6769    2.0495 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8351    1.0897   -0.5780 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2440   -0.9854    0.6051 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8870   -1.7315    0.6000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2815    1.2928    0.1691 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6126    1.2193    0.1104 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6349    0.8120   -2.0600 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4137   -0.1036   -0.7339 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4891   -1.9954   -1.4403 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9642   -1.7694    0.1321 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1603    0.1718    1.8951 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1640   -1.1481    1.5183 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8461    1.5813    1.6412 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 11 14  1  0
 14 15  1  0
 14 16  1  0
 16 17  1  0
  7  2  1  0
 16  9  1  0
  4 18  1  0
  5 19  1  0
  6 20  1  0
  9 21  1  0
 11 22  1  0
 12 23  1  0
 12 24  1  0
 13 25  1  0
 14 26  1  0
 15 27  1  0
 16 28  1  0
 17 29  1  0
M  END


  Mrv1652309112121092D          

 17 18  0  0  0  0            999 V2000
    0.1067    2.4134    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6078    2.0009    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3222    2.4134    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3222    3.2384    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0367    3.6509    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6078    3.6509    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.1067    3.2384    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0367    2.0009    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0367    1.1759    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3693    0.6910    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6242   -0.0937    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4492   -0.0937    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7041    0.6910    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9341   -0.7611    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5986   -1.5148    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1393   -0.7611    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5846    0.9459    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  4  6  1  0  0  0  0
  6  7  2  0  0  0  0
  1  7  1  0  0  0  0
  3  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
  9 13  1  0  0  0  0
 12 14  1  0  0  0  0
 14 15  1  0  0  0  0
 11 16  1  0  0  0  0
 10 17  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0257989

> <DATABASE_NAME>
hmdb

> <SMILES>
OCC1OC(ON2C=CC=NC2=O)C(O)C1O

> <INCHI_IDENTIFIER>
InChI=1S/C9H12N2O6/c12-4-5-6(13)7(14)8(16-5)17-11-3-1-2-10-9(11)15/h1-3,5-8,12-14H,4H2

> <INCHI_KEY>
BGSCNPOVJFBBAQ-UHFFFAOYSA-N

> <FORMULA>
C9H12N2O6

> <MOLECULAR_WEIGHT>
244.203

> <EXACT_MASS>
244.069536114

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
29

> <JCHEM_AVERAGE_POLARIZABILITY>
21.97617019233076

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1-{[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy}-1,2-dihydropyrimidin-2-one

> <ALOGPS_LOGP>
-1.18

> <JCHEM_LOGP>
-2.05525466

> <ALOGPS_LOGS>
-0.76

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.816561552592244

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.22650821404956

> <JCHEM_PKA_STRONGEST_BASIC>
-2.981183280513787

> <JCHEM_POLAR_SURFACE_AREA>
111.82000000000002

> <JCHEM_REFRACTIVITY>
53.0253

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.27e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1-{[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy}pyrimidin-2-one

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0257989
     RDKit          3D
1-[(2R,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxypyrimidin-2-one
 29 30  0  0  0  0  0  0  0  0999 V2000
    1.6144    1.6538   -1.7791 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5437    1.0076   -1.1872 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8152    1.4180   -1.1894 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.8072    0.7563   -0.5752 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4810   -0.4060    0.0884 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1665   -0.8055    0.0751 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1908   -0.1090   -0.5576 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.9042   -0.5367   -0.5475 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1596    0.2965   -0.1244 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1409    0.4112   -1.0693 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3590    0.3095   -0.4502 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4935   -0.0141   -1.3655 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3418   -1.2190   -2.0338 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1145   -0.7876    0.5777 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0865   -0.7601    1.5712 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7552   -0.3252    1.1107 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0344    0.6769    2.0495 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8351    1.0897   -0.5780 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2440   -0.9854    0.6051 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8870   -1.7315    0.6000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2815    1.2928    0.1691 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6126    1.2193    0.1104 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6349    0.8120   -2.0600 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4137   -0.1036   -0.7339 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4891   -1.9954   -1.4403 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9642   -1.7694    0.1321 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1603    0.1718    1.8951 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1640   -1.1481    1.5183 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8461    1.5813    1.6412 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 11 14  1  0
 14 15  1  0
 14 16  1  0
 16 17  1  0
  7  2  1  0
 16  9  1  0
  4 18  1  0
  5 19  1  0
  6 20  1  0
  9 21  1  0
 11 22  1  0
 12 23  1  0
 12 24  1  0
 13 25  1  0
 14 26  1  0
 15 27  1  0
 16 28  1  0
 17 29  1  0
M  END

HEADER    PROTEIN                                 11-SEP-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-21         0                                  
HETATM    1  C   UNK     0       0.199   4.505   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.134   3.735   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0      -2.468   4.505   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0      -2.468   6.045   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      -3.802   6.815   0.000  0.00  0.00           O+0
HETATM    6  N   UNK     0      -1.134   6.815   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0       0.199   6.045   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -3.802   3.735   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      -3.802   2.195   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -2.556   1.290   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -3.032  -0.175   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -4.572  -0.175   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      -5.048   1.290   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0      -5.477  -1.421   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      -4.851  -2.828   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0      -2.127  -1.421   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0      -1.091   1.766   0.000  0.00  0.00           O+0
CONECT    1    2    7                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4    8                                                  
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7                                                       
CONECT    7    6    1                                                       
CONECT    8    3    9                                                       
CONECT    9    8   10   13                                                  
CONECT   10    9   11   17                                                  
CONECT   11   10   12   16                                                  
CONECT   12   11   13   14                                                  
CONECT   13   12    9                                                       
CONECT   14   12   15                                                       
CONECT   15   14                                                            
CONECT   16   11                                                            
CONECT   17   10                                                            
MASTER        0    0    0    0    0    0    0    0   17    0   36    0
END

COMPND    HMDB0257989
HETATM    1  O1  UNL     1       1.614   1.654  -1.779  1.00  0.00           O  
HETATM    2  C1  UNL     1       2.544   1.008  -1.187  1.00  0.00           C  
HETATM    3  N1  UNL     1       3.815   1.418  -1.189  1.00  0.00           N  
HETATM    4  C2  UNL     1       4.807   0.756  -0.575  1.00  0.00           C  
HETATM    5  C3  UNL     1       4.481  -0.406   0.088  1.00  0.00           C  
HETATM    6  C4  UNL     1       3.166  -0.805   0.075  1.00  0.00           C  
HETATM    7  N2  UNL     1       2.191  -0.109  -0.558  1.00  0.00           N  
HETATM    8  O2  UNL     1       0.904  -0.537  -0.548  1.00  0.00           O  
HETATM    9  C5  UNL     1      -0.160   0.296  -0.124  1.00  0.00           C  
HETATM   10  O3  UNL     1      -1.141   0.411  -1.069  1.00  0.00           O  
HETATM   11  C6  UNL     1      -2.359   0.310  -0.450  1.00  0.00           C  
HETATM   12  C7  UNL     1      -3.494  -0.014  -1.365  1.00  0.00           C  
HETATM   13  O4  UNL     1      -3.342  -1.219  -2.034  1.00  0.00           O  
HETATM   14  C8  UNL     1      -2.115  -0.788   0.578  1.00  0.00           C  
HETATM   15  O5  UNL     1      -3.087  -0.760   1.571  1.00  0.00           O  
HETATM   16  C9  UNL     1      -0.755  -0.325   1.111  1.00  0.00           C  
HETATM   17  O6  UNL     1      -1.034   0.677   2.049  1.00  0.00           O  
HETATM   18  H1  UNL     1       5.835   1.090  -0.578  1.00  0.00           H  
HETATM   19  H2  UNL     1       5.244  -0.985   0.605  1.00  0.00           H  
HETATM   20  H3  UNL     1       2.887  -1.732   0.600  1.00  0.00           H  
HETATM   21  H4  UNL     1       0.282   1.293   0.169  1.00  0.00           H  
HETATM   22  H5  UNL     1      -2.613   1.219   0.110  1.00  0.00           H  
HETATM   23  H6  UNL     1      -3.635   0.812  -2.060  1.00  0.00           H  
HETATM   24  H7  UNL     1      -4.414  -0.104  -0.734  1.00  0.00           H  
HETATM   25  H8  UNL     1      -3.489  -1.995  -1.440  1.00  0.00           H  
HETATM   26  H9  UNL     1      -1.964  -1.769   0.132  1.00  0.00           H  
HETATM   27  H10 UNL     1      -3.160   0.172   1.895  1.00  0.00           H  
HETATM   28  H11 UNL     1      -0.164  -1.148   1.518  1.00  0.00           H  
HETATM   29  H12 UNL     1      -0.846   1.581   1.641  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    7
CONECT    3    4    4
CONECT    4    5   18
CONECT    5    6    6   19
CONECT    6    7   20
CONECT    7    8
CONECT    8    9
CONECT    9   10   16   21
CONECT   10   11
CONECT   11   12   14   22
CONECT   12   13   23   24
CONECT   13   25
CONECT   14   15   16   26
CONECT   15   27
CONECT   16   17   28
CONECT   17   29
END

HMDB0257989
     RDKit          3D
1-[(2R,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxypyrimidin-2-one
 29 30  0  0  0  0  0  0  0  0999 V2000
    1.6144    1.6538   -1.7791 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5437    1.0076   -1.1872 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8152    1.4180   -1.1894 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.8072    0.7563   -0.5752 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4810   -0.4060    0.0884 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1665   -0.8055    0.0751 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1908   -0.1090   -0.5576 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.9042   -0.5367   -0.5475 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1596    0.2965   -0.1244 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1409    0.4112   -1.0693 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3590    0.3095   -0.4502 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4935   -0.0141   -1.3655 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3418   -1.2190   -2.0338 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1145   -0.7876    0.5777 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0865   -0.7601    1.5712 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7552   -0.3252    1.1107 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0344    0.6769    2.0495 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8351    1.0897   -0.5780 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2440   -0.9854    0.6051 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8870   -1.7315    0.6000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2815    1.2928    0.1691 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6126    1.2193    0.1104 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6349    0.8120   -2.0600 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4137   -0.1036   -0.7339 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4891   -1.9954   -1.4403 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9642   -1.7694    0.1321 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1603    0.1718    1.8951 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1640   -1.1481    1.5183 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8461    1.5813    1.6412 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 11 14  1  0
 14 15  1  0
 14 16  1  0
 16 17  1  0
  7  2  1  0
 16  9  1  0
  4 18  1  0
  5 19  1  0
  6 20  1  0
  9 21  1  0
 11 22  1  0
 12 23  1  0
 12 24  1  0
 13 25  1  0
 14 26  1  0
 15 27  1  0
 16 28  1  0
 17 29  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Not Available

Chemical Formula

C₉H₁₂N₂O₆

Average Molecular Weight

244.203

Monoisotopic Molecular Weight

244.069536114

IUPAC Name

1-{[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy}-1,2-dihydropyrimidin-2-one

Traditional Name

1-{[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy}pyrimidin-2-one

CAS Registry Number

Not Available

SMILES

OCC1OC(ON2C=CC=NC2=O)C(O)C1O

InChI Identifier

InChI=1S/C9H12N2O6/c12-4-5-6(13)7(14)8(16-5)17-11-3-1-2-10-9(11)15/h1-3,5-8,12-14H,4H2

InChI Key

BGSCNPOVJFBBAQ-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Pentoses

Alternative Parents

Substituents

Pentose monosaccharide
Pyrimidone
Pyrimidine
Hydropyrimidine
Heteroaromatic compound
Tetrahydrofuran
Secondary alcohol
Oxacycle
Azacycle
Organoheterocyclic compound
Organic nitrogen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Primary alcohol
Organonitrogen compound
Alcohol
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 31557052)

Source

Exogenous

Exogenous (PMID: 31557052)

Process

Not Available

Role

Not Available

Physical Properties

State

Not Available

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
logP	-1.2	ALOGPS
logP	-2.1	ChemAxon
logS	-0.76	ALOGPS
pKa (Strongest Acidic)	12.23	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	111.82 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	53.03 m³·mol⁻¹	ChemAxon
Polarizability	21.98 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DeepCCS	[M+H]+	148.628	30932474
DeepCCS	[M-H]-	146.27	30932474
DeepCCS	[M-2H]-	180.263	30932474
DeepCCS	[M+Na]+	155.171	30932474

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.	2.37 minutes	32390414
Predicted by Siyang on May 30, 2022	8.9667 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	4.65 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	590.6 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	246.7 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	58.2 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	159.3 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	46.8 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	278.0 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	251.9 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	393.1 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	567.8 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	43.9 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	808.2 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	165.9 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	216.1 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	546.5 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	237.4 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	226.6 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
1-[(2R,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxypyrimidin-2-one	OCC1OC(ON2C=CC=NC2=O)C(O)C1O	3152.5	Standard polar	33892256
1-[(2R,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxypyrimidin-2-one	OCC1OC(ON2C=CC=NC2=O)C(O)C1O	2418.7	Standard non polar	33892256
1-[(2R,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxypyrimidin-2-one	OCC1OC(ON2C=CC=NC2=O)C(O)C1O	2368.1	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 - 1-[(2R,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxypyrimidin-2-one GC-MS (Non-derivatized) - 70eV, Positive	splash10-0bt9-9210000000-24a8bedba928eda4adc3	2021-09-23	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 1-[(2R,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxypyrimidin-2-one GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 1-[(2R,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxypyrimidin-2-one GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 1-[(2R,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxypyrimidin-2-one GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 1-[(2R,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxypyrimidin-2-one GC-MS (TMS_1_3) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 1-[(2R,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxypyrimidin-2-one GC-MS (TMS_2_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 1-[(2R,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxypyrimidin-2-one GC-MS (TMS_2_2) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 1-[(2R,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxypyrimidin-2-one GC-MS (TMS_2_3) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 1-[(2R,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxypyrimidin-2-one GC-MS (TMS_3_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 1-[(2R,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxypyrimidin-2-one GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 1-[(2R,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxypyrimidin-2-one GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 1-[(2R,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxypyrimidin-2-one GC-MS (TBDMS_1_3) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 1-[(2R,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxypyrimidin-2-one GC-MS (TBDMS_2_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 1-[(2R,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxypyrimidin-2-one GC-MS (TBDMS_2_2) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 1-[(2R,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxypyrimidin-2-one GC-MS (TBDMS_2_3) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 1-[(2R,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxypyrimidin-2-one GC-MS (TBDMS_3_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	31557052	details

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

76059428

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]

Showing metabocard for 1-[(2R,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxypyrimidin-2-one (HMDB0257989)

MOL for HMDB0257989 (1-[(2R,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxypyrimidin-2-one)

3D MOL for HMDB0257989 (1-[(2R,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxypyrimidin-2-one)

3D SDF for HMDB0257989 (1-[(2R,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxypyrimidin-2-one)

3D-SDF for HMDB0257989 (1-[(2R,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxypyrimidin-2-one)

PDB for HMDB0257989 (1-[(2R,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxypyrimidin-2-one)

3D PDB for HMDB0257989 (1-[(2R,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxypyrimidin-2-one)

SMILES for HMDB0257989 (1-[(2R,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxypyrimidin-2-one)

INCHI for HMDB0257989 (1-[(2R,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxypyrimidin-2-one)

Structure for HMDB0257989 (1-[(2R,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxypyrimidin-2-one)

3D Structure for HMDB0257989 (1-[(2R,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxypyrimidin-2-one)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra