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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-12 00:34:52 UTC

Update Date

2021-09-26 23:18:27 UTC

HMDB ID

HMDB0260369

Secondary Accession Numbers

None

Metabolite Identification

Common Name

6-[(2R,4S,5R)-4-Hydroxy-5-(hydroxymethyl)oxolan-2-yl]-7,8-dihydroimidazo[1,2-c]pyrimidin-5-one

Description

6-[(2R,4S,5R)-4-Hydroxy-5-(hydroxymethyl)oxolan-2-yl]-7,8-dihydroimidazo[1,2-c]pyrimidin-5-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 6-[(2R,4S,5R)-4-Hydroxy-5-(hydroxymethyl)oxolan-2-yl]-7,8-dihydroimidazo[1,2-c]pyrimidin-5-one. This compound has been identified in human blood as reported by (PMID: 31557052 ). 6-[(2r,4s,5r)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-7,8-dihydroimidazo[1,2-c]pyrimidin-5-one is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 6-[(2R,4S,5R)-4-Hydroxy-5-(hydroxymethyl)oxolan-2-yl]-7,8-dihydroimidazo[1,2-c]pyrimidin-5-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

HMDB0260369
     RDKit          3D
6-[(2R,4S,5R)-4-Hydroxy-5-(hydroxymethyl)oxolan-2-yl]-7,8-dihydroimidazo[1,2-...
 33 35  0  0  0  0  0  0  0  0999 V2000
    1.7370   -1.7461   -1.6828 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8277   -0.7709   -0.8933 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6400   -0.0753   -0.4970 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6446   -0.6701   -0.5476 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3064   -0.7560    0.8353 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6999   -1.1567    0.3820 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6658   -0.8674    1.3329 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8336   -0.3337   -0.8683 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6328    0.9352   -0.6157 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0452    1.7221    0.3649 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5790    0.0418   -1.2765 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8634    1.2877   -0.0407 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0363    1.3597    0.8727 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2362    0.6286    0.4129 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5621    0.7770    0.6868 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.2817   -0.1441    0.0331 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3637   -0.8873   -0.6697 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1137   -0.3965   -0.4232 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6210   -1.7130   -0.9215 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3091    0.2183    1.3434 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8224   -1.5673    1.4110 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6702   -2.2406    0.1244 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7201   -1.6506    1.9388 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2959   -0.9382   -1.6434 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6569    1.5421   -1.5415 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6900    0.7008   -0.3731 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4916    1.5449    1.2267 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1080    1.8889   -0.9565 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0303    1.7375    0.3949 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7221    1.0511    1.8911 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3218    2.4510    0.9439 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3554   -0.2601    0.0657 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5459   -1.7130   -1.3095 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  1  0
  9 10  1  0
  8 11  1  0
  3 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  2  0
 15 16  1  0
 16 17  2  0
 17 18  1  0
 18  2  1  0
 11  4  1  0
 18 14  1  0
  4 19  1  0
  5 20  1  0
  5 21  1  0
  6 22  1  0
  7 23  1  0
  8 24  1  0
  9 25  1  0
  9 26  1  0
 10 27  1  0
 12 28  1  0
 12 29  1  0
 13 30  1  0
 13 31  1  0
 16 32  1  0
 17 33  1  0
M  END


  Mrv1652309122102352D          

 18 20  0  0  0  0            999 V2000
    3.2789    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.2789   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2789   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5645    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.5645    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7798    1.0799    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2949    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7798   -0.2549    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7079   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4615   -0.0769    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0136   -0.6900    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6011   -1.4045    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7941   -1.2330    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.9366   -2.1582    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7571   -2.2444    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.8341   -0.6038    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  4  6  1  0  0  0  0
  6  7  1  0  0  0  0
  1  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
  6 10  1  0  0  0  0
  3 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 11 15  1  0  0  0  0
 14 16  1  0  0  0  0
 16 17  1  0  0  0  0
 13 18  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0260369

> <DATABASE_NAME>
hmdb

> <SMILES>
OCC1OC(CC1O)N1CCC2=NC=CN2C1=O

> <INCHI_IDENTIFIER>
InChI=1S/C11H15N3O4/c15-6-8-7(16)5-10(18-8)14-3-1-9-12-2-4-13(9)11(14)17/h2,4,7-8,10,15-16H,1,3,5-6H2

> <INCHI_KEY>
DKGALSINFDGMOW-UHFFFAOYSA-N

> <FORMULA>
C11H15N3O4

> <MOLECULAR_WEIGHT>
253.258

> <EXACT_MASS>
253.106255975

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
33

> <JCHEM_AVERAGE_POLARIZABILITY>
25.196679118970042

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
6-[4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5H,6H,7H,8H-imidazo[1,2-c]pyrimidin-5-one

> <ALOGPS_LOGP>
-1.24

> <JCHEM_LOGP>
-1.533191154666667

> <ALOGPS_LOGS>
-0.94

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.787699230192263

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.895427790145998

> <JCHEM_PKA_STRONGEST_BASIC>
2.3057510845551157

> <JCHEM_POLAR_SURFACE_AREA>
87.82000000000001

> <JCHEM_REFRACTIVITY>
59.5231

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.89e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
6-[4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-7H,8H-imidazo[1,2-c]pyrimidin-5-one

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0260369
     RDKit          3D
6-[(2R,4S,5R)-4-Hydroxy-5-(hydroxymethyl)oxolan-2-yl]-7,8-dihydroimidazo[1,2-...
 33 35  0  0  0  0  0  0  0  0999 V2000
    1.7370   -1.7461   -1.6828 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8277   -0.7709   -0.8933 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6400   -0.0753   -0.4970 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6446   -0.6701   -0.5476 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3064   -0.7560    0.8353 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6999   -1.1567    0.3820 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6658   -0.8674    1.3329 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8336   -0.3337   -0.8683 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6328    0.9352   -0.6157 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0452    1.7221    0.3649 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5790    0.0418   -1.2765 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8634    1.2877   -0.0407 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0363    1.3597    0.8727 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2362    0.6286    0.4129 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5621    0.7770    0.6868 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.2817   -0.1441    0.0331 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3637   -0.8873   -0.6697 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1137   -0.3965   -0.4232 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6210   -1.7130   -0.9215 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3091    0.2183    1.3434 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8224   -1.5673    1.4110 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6702   -2.2406    0.1244 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7201   -1.6506    1.9388 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2959   -0.9382   -1.6434 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6569    1.5421   -1.5415 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6900    0.7008   -0.3731 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4916    1.5449    1.2267 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1080    1.8889   -0.9565 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0303    1.7375    0.3949 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7221    1.0511    1.8911 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3218    2.4510    0.9439 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3554   -0.2601    0.0657 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5459   -1.7130   -1.3095 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  1  0
  9 10  1  0
  8 11  1  0
  3 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  2  0
 15 16  1  0
 16 17  2  0
 17 18  1  0
 18  2  1  0
 11  4  1  0
 18 14  1  0
  4 19  1  0
  5 20  1  0
  5 21  1  0
  6 22  1  0
  7 23  1  0
  8 24  1  0
  9 25  1  0
  9 26  1  0
 10 27  1  0
 12 28  1  0
 12 29  1  0
 13 30  1  0
 13 31  1  0
 16 32  1  0
 17 33  1  0
M  END

HEADER    PROTEIN                                 12-SEP-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   12-SEP-21         0                                  
HETATM    1  C   UNK     0       6.121   2.310   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       7.454   1.540   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0       7.454   0.000   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0       6.121  -0.770   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       6.121  -2.310   0.000  0.00  0.00           O+0
HETATM    6  N   UNK     0       4.787   0.000   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0       4.787   1.540   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0       3.322   2.016   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0       2.417   0.770   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       3.322  -0.476   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       8.788  -0.770   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      10.195  -0.144   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      11.225  -1.288   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      10.455  -2.622   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       8.949  -2.302   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      11.082  -4.029   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0      12.613  -4.190   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0      12.757  -1.127   0.000  0.00  0.00           O+0
CONECT    1    2    7                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4   11                                                  
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7   10                                                  
CONECT    7    6    1    8                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9    6                                                       
CONECT   11    3   12   15                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14   18                                                  
CONECT   14   13   15   16                                                  
CONECT   15   14   11                                                       
CONECT   16   14   17                                                       
CONECT   17   16                                                            
CONECT   18   13                                                            
MASTER        0    0    0    0    0    0    0    0   18    0   40    0
END

COMPND    HMDB0260369
HETATM    1  O1  UNL     1       1.737  -1.746  -1.683  1.00  0.00           O  
HETATM    2  C1  UNL     1       1.828  -0.771  -0.893  1.00  0.00           C  
HETATM    3  N1  UNL     1       0.640  -0.075  -0.497  1.00  0.00           N  
HETATM    4  C2  UNL     1      -0.645  -0.670  -0.548  1.00  0.00           C  
HETATM    5  C3  UNL     1      -1.306  -0.756   0.835  1.00  0.00           C  
HETATM    6  C4  UNL     1      -2.700  -1.157   0.382  1.00  0.00           C  
HETATM    7  O2  UNL     1      -3.666  -0.867   1.333  1.00  0.00           O  
HETATM    8  C5  UNL     1      -2.834  -0.334  -0.868  1.00  0.00           C  
HETATM    9  C6  UNL     1      -3.633   0.935  -0.616  1.00  0.00           C  
HETATM   10  O3  UNL     1      -3.045   1.722   0.365  1.00  0.00           O  
HETATM   11  O4  UNL     1      -1.579   0.042  -1.276  1.00  0.00           O  
HETATM   12  C7  UNL     1       0.863   1.288  -0.041  1.00  0.00           C  
HETATM   13  C8  UNL     1       2.036   1.360   0.873  1.00  0.00           C  
HETATM   14  C9  UNL     1       3.236   0.629   0.413  1.00  0.00           C  
HETATM   15  N2  UNL     1       4.562   0.777   0.687  1.00  0.00           N  
HETATM   16  C10 UNL     1       5.282  -0.144   0.033  1.00  0.00           C  
HETATM   17  C11 UNL     1       4.364  -0.887  -0.670  1.00  0.00           C  
HETATM   18  N3  UNL     1       3.114  -0.396  -0.423  1.00  0.00           N  
HETATM   19  H1  UNL     1      -0.621  -1.713  -0.922  1.00  0.00           H  
HETATM   20  H2  UNL     1      -1.309   0.218   1.343  1.00  0.00           H  
HETATM   21  H3  UNL     1      -0.822  -1.567   1.411  1.00  0.00           H  
HETATM   22  H4  UNL     1      -2.670  -2.241   0.124  1.00  0.00           H  
HETATM   23  H5  UNL     1      -3.720  -1.651   1.939  1.00  0.00           H  
HETATM   24  H6  UNL     1      -3.296  -0.938  -1.643  1.00  0.00           H  
HETATM   25  H7  UNL     1      -3.657   1.542  -1.542  1.00  0.00           H  
HETATM   26  H8  UNL     1      -4.690   0.701  -0.373  1.00  0.00           H  
HETATM   27  H9  UNL     1      -3.492   1.545   1.227  1.00  0.00           H  
HETATM   28  H10 UNL     1       1.108   1.889  -0.957  1.00  0.00           H  
HETATM   29  H11 UNL     1      -0.030   1.737   0.395  1.00  0.00           H  
HETATM   30  H12 UNL     1       1.722   1.051   1.891  1.00  0.00           H  
HETATM   31  H13 UNL     1       2.322   2.451   0.944  1.00  0.00           H  
HETATM   32  H14 UNL     1       6.355  -0.260   0.066  1.00  0.00           H  
HETATM   33  H15 UNL     1       4.546  -1.713  -1.309  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3   18
CONECT    3    4   12
CONECT    4    5   11   19
CONECT    5    6   20   21
CONECT    6    7    8   22
CONECT    7   23
CONECT    8    9   11   24
CONECT    9   10   25   26
CONECT   10   27
CONECT   12   13   28   29
CONECT   13   14   30   31
CONECT   14   15   15   18
CONECT   15   16
CONECT   16   17   17   32
CONECT   17   18   33
END

HMDB0260369
     RDKit          3D
6-[(2R,4S,5R)-4-Hydroxy-5-(hydroxymethyl)oxolan-2-yl]-7,8-dihydroimidazo[1,2-...
 33 35  0  0  0  0  0  0  0  0999 V2000
    1.7370   -1.7461   -1.6828 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8277   -0.7709   -0.8933 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6400   -0.0753   -0.4970 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6446   -0.6701   -0.5476 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3064   -0.7560    0.8353 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6999   -1.1567    0.3820 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6658   -0.8674    1.3329 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8336   -0.3337   -0.8683 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6328    0.9352   -0.6157 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0452    1.7221    0.3649 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5790    0.0418   -1.2765 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8634    1.2877   -0.0407 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0363    1.3597    0.8727 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2362    0.6286    0.4129 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5621    0.7770    0.6868 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.2817   -0.1441    0.0331 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3637   -0.8873   -0.6697 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1137   -0.3965   -0.4232 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6210   -1.7130   -0.9215 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3091    0.2183    1.3434 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8224   -1.5673    1.4110 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6702   -2.2406    0.1244 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7201   -1.6506    1.9388 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2959   -0.9382   -1.6434 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6569    1.5421   -1.5415 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6900    0.7008   -0.3731 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4916    1.5449    1.2267 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1080    1.8889   -0.9565 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0303    1.7375    0.3949 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7221    1.0511    1.8911 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3218    2.4510    0.9439 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3554   -0.2601    0.0657 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5459   -1.7130   -1.3095 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  1  0
  9 10  1  0
  8 11  1  0
  3 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  2  0
 15 16  1  0
 16 17  2  0
 17 18  1  0
 18  2  1  0
 11  4  1  0
 18 14  1  0
  4 19  1  0
  5 20  1  0
  5 21  1  0
  6 22  1  0
  7 23  1  0
  8 24  1  0
  9 25  1  0
  9 26  1  0
 10 27  1  0
 12 28  1  0
 12 29  1  0
 13 30  1  0
 13 31  1  0
 16 32  1  0
 17 33  1  0
M  END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Not Available

Chemical Formula

C₁₁H₁₅N₃O₄

Average Molecular Weight

253.258

Monoisotopic Molecular Weight

253.106255975

IUPAC Name

6-[4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5H,6H,7H,8H-imidazo[1,2-c]pyrimidin-5-one

Traditional Name

6-[4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-7H,8H-imidazo[1,2-c]pyrimidin-5-one

CAS Registry Number

Not Available

SMILES

OCC1OC(CC1O)N1CCC2=NC=CN2C1=O

InChI Identifier

InChI=1S/C11H15N3O4/c15-6-8-7(16)5-10(18-8)14-3-1-9-12-2-4-13(9)11(14)17/h2,4,7-8,10,15-16H,1,3,5-6H2

InChI Key

DKGALSINFDGMOW-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
Imidazopyrimidinone
Pyrimidone
Pyrimidine
N-substituted imidazole
Heteroaromatic compound
Tetrahydrofuran
Imidazole
Azole
Urea
Secondary alcohol
Carbonic acid derivative
Oxacycle
Azacycle
Organoheterocyclic compound
Organic nitrogen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Primary alcohol
Organonitrogen compound
Alcohol
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic 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	-1.5	ChemAxon
logS	-0.94	ALOGPS
pKa (Strongest Acidic)	13.9	ChemAxon
pKa (Strongest Basic)	2.31	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	87.82 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	59.52 m³·mol⁻¹	ChemAxon
Polarizability	25.2 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
AllCCS	[M+H]+	158.004	32859911
AllCCS	[M+H-H2O]+	154.328	32859911
AllCCS	[M+Na]+	162.398	32859911
AllCCS	[M+NH4]+	161.417	32859911
AllCCS	[M-H]-	158.478	32859911
AllCCS	[M+Na-2H]-	158.155	32859911
AllCCS	[M+HCOO]-	157.908	32859911
DeepCCS	[M+H]+	150.86	30932474
DeepCCS	[M-H]-	148.502	30932474
DeepCCS	[M-2H]-	183.309	30932474
DeepCCS	[M+Na]+	159.189	30932474

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
6-[(2R,4S,5R)-4-Hydroxy-5-(hydroxymethyl)oxolan-2-yl]-7,8-dihydroimidazo[1,2-c]pyrimidin-5-one	OCC1OC(CC1O)N1CCC2=NC=CN2C1=O	3585.2	Standard polar	33892256
6-[(2R,4S,5R)-4-Hydroxy-5-(hydroxymethyl)oxolan-2-yl]-7,8-dihydroimidazo[1,2-c]pyrimidin-5-one	OCC1OC(CC1O)N1CCC2=NC=CN2C1=O	2069.1	Standard non polar	33892256
6-[(2R,4S,5R)-4-Hydroxy-5-(hydroxymethyl)oxolan-2-yl]-7,8-dihydroimidazo[1,2-c]pyrimidin-5-one	OCC1OC(CC1O)N1CCC2=NC=CN2C1=O	2537.2	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 - 6-[(2R,4S,5R)-4-Hydroxy-5-(hydroxymethyl)oxolan-2-yl]-7,8-dihydroimidazo[1,2-c]pyrimidin-5-one GC-MS (Non-derivatized) - 70eV, Positive	splash10-0006-9340000000-c2e5a81980c8c922226c	2021-09-23	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 6-[(2R,4S,5R)-4-Hydroxy-5-(hydroxymethyl)oxolan-2-yl]-7,8-dihydroimidazo[1,2-c]pyrimidin-5-one GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 6-[(2R,4S,5R)-4-Hydroxy-5-(hydroxymethyl)oxolan-2-yl]-7,8-dihydroimidazo[1,2-c]pyrimidin-5-one GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 6-[(2R,4S,5R)-4-Hydroxy-5-(hydroxymethyl)oxolan-2-yl]-7,8-dihydroimidazo[1,2-c]pyrimidin-5-one GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 6-[(2R,4S,5R)-4-Hydroxy-5-(hydroxymethyl)oxolan-2-yl]-7,8-dihydroimidazo[1,2-c]pyrimidin-5-one GC-MS (TMS_2_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 6-[(2R,4S,5R)-4-Hydroxy-5-(hydroxymethyl)oxolan-2-yl]-7,8-dihydroimidazo[1,2-c]pyrimidin-5-one GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 6-[(2R,4S,5R)-4-Hydroxy-5-(hydroxymethyl)oxolan-2-yl]-7,8-dihydroimidazo[1,2-c]pyrimidin-5-one GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 6-[(2R,4S,5R)-4-Hydroxy-5-(hydroxymethyl)oxolan-2-yl]-7,8-dihydroimidazo[1,2-c]pyrimidin-5-one GC-MS (TBDMS_2_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-10-27	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-10-27	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-10-27	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-10-27	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-10-27	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-10-27	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-10-27	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-10-27	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-10-27	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-10-27	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-10-27	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-10-27	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-10-27	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-10-27	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-10-27	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-10-27	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-10-27	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-10-27	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-10-27	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-10-27	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

76066936

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 6-[(2R,4S,5R)-4-Hydroxy-5-(hydroxymethyl)oxolan-2-yl]-7,8-dihydroimidazo[1,2-c]pyrimidin-5-one (HMDB0260369)

MOL for HMDB0260369 (6-[(2R,4S,5R)-4-Hydroxy-5-(hydroxymethyl)oxolan-2-yl]-7,8-dihydroimidazo[1,2-c]pyrimidin-5-one)

3D MOL for HMDB0260369 (6-[(2R,4S,5R)-4-Hydroxy-5-(hydroxymethyl)oxolan-2-yl]-7,8-dihydroimidazo[1,2-c]pyrimidin-5-one)

3D SDF for HMDB0260369 (6-[(2R,4S,5R)-4-Hydroxy-5-(hydroxymethyl)oxolan-2-yl]-7,8-dihydroimidazo[1,2-c]pyrimidin-5-one)

3D-SDF for HMDB0260369 (6-[(2R,4S,5R)-4-Hydroxy-5-(hydroxymethyl)oxolan-2-yl]-7,8-dihydroimidazo[1,2-c]pyrimidin-5-one)

PDB for HMDB0260369 (6-[(2R,4S,5R)-4-Hydroxy-5-(hydroxymethyl)oxolan-2-yl]-7,8-dihydroimidazo[1,2-c]pyrimidin-5-one)

3D PDB for HMDB0260369 (6-[(2R,4S,5R)-4-Hydroxy-5-(hydroxymethyl)oxolan-2-yl]-7,8-dihydroimidazo[1,2-c]pyrimidin-5-one)

SMILES for HMDB0260369 (6-[(2R,4S,5R)-4-Hydroxy-5-(hydroxymethyl)oxolan-2-yl]-7,8-dihydroimidazo[1,2-c]pyrimidin-5-one)

INCHI for HMDB0260369 (6-[(2R,4S,5R)-4-Hydroxy-5-(hydroxymethyl)oxolan-2-yl]-7,8-dihydroimidazo[1,2-c]pyrimidin-5-one)

Structure for HMDB0260369 (6-[(2R,4S,5R)-4-Hydroxy-5-(hydroxymethyl)oxolan-2-yl]-7,8-dihydroimidazo[1,2-c]pyrimidin-5-one)

3D Structure for HMDB0260369 (6-[(2R,4S,5R)-4-Hydroxy-5-(hydroxymethyl)oxolan-2-yl]-7,8-dihydroimidazo[1,2-c]pyrimidin-5-one)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

NMR Spectra