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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-10 23:46:14 UTC

Update Date

2021-09-26 22:56:02 UTC

HMDB ID

HMDB0246756

Secondary Accession Numbers

None

Metabolite Identification

Common Name

5-Benzylacyclouridine

Description

5-Benzylacyclouridine, also known as BAU or 5-BACU, belongs to the class of organic compounds known as pyrimidones. Pyrimidones are compounds that contain a pyrimidine ring, which bears a ketone. Pyrimidine is a 6-membered ring consisting of four carbon atoms and two nitrogen centers at the 1- and 3- ring positions. Based on a literature review a significant number of articles have been published on 5-Benzylacyclouridine. This compound has been identified in human blood as reported by (PMID: 31557052 ). 5-benzylacyclouridine is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 5-Benzylacyclouridine 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

HMDB0246756
     RDKit          3D
5-Benzylacyclouridine
 36 37  0  0  0  0  0  0  0  0999 V2000
   -1.4798   -2.4392   -1.2745 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6079   -1.5867   -0.9472 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4759   -1.3459   -1.7030 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4198   -0.4282   -1.3540 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3660   -0.3064   -2.1432 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3231    0.2886   -0.2355 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.2881    1.2655    0.1995 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2702    0.8265    1.0190 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1957   -0.0564    0.5901 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1467    0.3968   -0.4634 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8642    1.4933    0.0368 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2262    0.0456    0.5298 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7489   -0.8754    0.2071 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9171   -1.0775    1.0915 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1348   -0.4216    0.5687 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3231    0.9433    0.8204 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4280    1.6171    0.3758 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3860    0.9416   -0.3397 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2490   -0.3909   -0.6116 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1222   -1.0560   -0.1523 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5838   -1.8868   -2.5819 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6703    1.8682   -0.6690 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7015    2.0346    0.7915 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8342   -0.3195    1.4879 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7637   -1.0363    0.2856 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7468    0.5861   -1.4583 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9201   -0.4164   -0.5935 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.6337    1.1638    0.5926 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1053    0.5968    1.4350 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1294   -2.1786    1.1944 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6440   -0.6955    2.0963 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5497    1.4521    1.3896 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5362    2.6579    0.5871 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2811    1.4322   -0.7150 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9912   -0.9712   -1.1806 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0068   -2.1214   -0.3582 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  2  0
  4  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
  6 12  1  0
 12 13  2  0
 13 14  1  0
 14 15  1  0
 15 16  2  0
 16 17  1  0
 17 18  2  0
 18 19  1  0
 19 20  2  0
 13  2  1  0
 20 15  1  0
  3 21  1  0
  7 22  1  0
  7 23  1  0
  9 24  1  0
  9 25  1  0
 10 26  1  0
 10 27  1  0
 11 28  1  0
 12 29  1  0
 14 30  1  0
 14 31  1  0
 16 32  1  0
 17 33  1  0
 18 34  1  0
 19 35  1  0
 20 36  1  0
M  END

BAU
  Mrv0541 02241213262D          

 20 21  0  0  0  0            999 V2000
   -4.4139   -0.7634    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6994   -0.3509    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9849   -0.7634    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2705   -0.3509    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5560   -0.7634    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8415   -0.3509    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8415    0.4741    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5560    0.8866    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1271    0.8866    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5874    0.4741    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3019    0.8866    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1271   -0.7634    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5874   -0.3509    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3019   -0.7634    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0164   -0.3509    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0164    0.4741    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7308    0.8866    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4453    0.4741    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4453   -0.3509    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7308   -0.7634    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  6 12  1  0  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 10 13  1  0  0  0  0
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 15 20  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
 18 19  1  0  0  0  0
 19 20  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0246756

> <DATABASE_NAME>
hmdb

> <SMILES>
OCCOCN1C=C(CC2=CC=CC=C2)C(=O)NC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C14H16N2O4/c17-6-7-20-10-16-9-12(13(18)15-14(16)19)8-11-4-2-1-3-5-11/h1-5,9,17H,6-8,10H2,(H,15,18,19)

> <INCHI_KEY>
SPJAGILXQBHHSZ-UHFFFAOYSA-N

> <FORMULA>
C14H16N2O4

> <MOLECULAR_WEIGHT>
276.2878

> <EXACT_MASS>
276.11100701

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
28.240570808849668

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
5-benzyl-1-[(2-hydroxyethoxy)methyl]-1,2,3,4-tetrahydropyrimidine-2,4-dione

> <ALOGPS_LOGP>
0.48

> <JCHEM_LOGP>
0.7153316146666666

> <ALOGPS_LOGS>
-2.53

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.119128878618994

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.948786592839104

> <JCHEM_PKA_STRONGEST_BASIC>
-2.7472465582463306

> <JCHEM_POLAR_SURFACE_AREA>
78.87

> <JCHEM_REFRACTIVITY>
72.06440000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.18e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-benzylacyclouridine

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0246756
     RDKit          3D
5-Benzylacyclouridine
 36 37  0  0  0  0  0  0  0  0999 V2000
   -1.4798   -2.4392   -1.2745 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6079   -1.5867   -0.9472 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4759   -1.3459   -1.7030 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4198   -0.4282   -1.3540 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3660   -0.3064   -2.1432 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3231    0.2886   -0.2355 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.2881    1.2655    0.1995 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2702    0.8265    1.0190 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1957   -0.0564    0.5901 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1467    0.3968   -0.4634 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8642    1.4933    0.0368 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2262    0.0456    0.5298 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7489   -0.8754    0.2071 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9171   -1.0775    1.0915 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1348   -0.4216    0.5687 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3231    0.9433    0.8204 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4280    1.6171    0.3758 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3860    0.9416   -0.3397 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2490   -0.3909   -0.6116 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1222   -1.0560   -0.1523 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5838   -1.8868   -2.5819 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6703    1.8682   -0.6690 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7015    2.0346    0.7915 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8342   -0.3195    1.4879 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7637   -1.0363    0.2856 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7468    0.5861   -1.4583 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9201   -0.4164   -0.5935 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.6337    1.1638    0.5926 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1053    0.5968    1.4350 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1294   -2.1786    1.1944 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6440   -0.6955    2.0963 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5497    1.4521    1.3896 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5362    2.6579    0.5871 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2811    1.4322   -0.7150 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9912   -0.9712   -1.1806 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0068   -2.1214   -0.3582 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  2  0
  4  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
  6 12  1  0
 12 13  2  0
 13 14  1  0
 14 15  1  0
 15 16  2  0
 16 17  1  0
 17 18  2  0
 18 19  1  0
 19 20  2  0
 13  2  1  0
 20 15  1  0
  3 21  1  0
  7 22  1  0
  7 23  1  0
  9 24  1  0
  9 25  1  0
 10 26  1  0
 10 27  1  0
 11 28  1  0
 12 29  1  0
 14 30  1  0
 14 31  1  0
 16 32  1  0
 17 33  1  0
 18 34  1  0
 19 35  1  0
 20 36  1  0
M  END

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: BAU                                               
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  O   UNK     0      -8.239  -1.425   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      -6.906  -0.655   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -5.572  -1.425   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      -4.238  -0.655   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0      -2.905  -1.425   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0      -1.571  -0.655   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0      -1.571   0.885   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -2.905   1.655   0.000  0.00  0.00           O+0
HETATM    9  N   UNK     0      -0.237   1.655   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0       1.096   0.885   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       2.430   1.655   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      -0.237  -1.425   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       1.096  -0.655   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       2.430  -1.425   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       3.764  -0.655   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       3.764   0.885   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       5.097   1.655   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       6.431   0.885   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       6.431  -0.655   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       5.097  -1.425   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7   12                                                  
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10                                                       
CONECT   10    9   11   13                                                  
CONECT   11   10                                                            
CONECT   12    6   13                                                       
CONECT   13   10   12   14                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16   20                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   15   19                                                       
MASTER        0    0    0    0    0    0    0    0   20    0   42    0
END

COMPND    HMDB0246756
HETATM    1  O1  UNL     1      -1.480  -2.439  -1.274  1.00  0.00           O  
HETATM    2  C1  UNL     1      -0.608  -1.587  -0.947  1.00  0.00           C  
HETATM    3  N1  UNL     1       0.476  -1.346  -1.703  1.00  0.00           N  
HETATM    4  C2  UNL     1       1.420  -0.428  -1.354  1.00  0.00           C  
HETATM    5  O2  UNL     1       2.366  -0.306  -2.143  1.00  0.00           O  
HETATM    6  N2  UNL     1       1.323   0.289  -0.236  1.00  0.00           N  
HETATM    7  C3  UNL     1       2.288   1.266   0.200  1.00  0.00           C  
HETATM    8  O3  UNL     1       3.270   0.827   1.019  1.00  0.00           O  
HETATM    9  C4  UNL     1       4.196  -0.056   0.590  1.00  0.00           C  
HETATM   10  C5  UNL     1       5.147   0.397  -0.463  1.00  0.00           C  
HETATM   11  O4  UNL     1       5.864   1.493   0.037  1.00  0.00           O  
HETATM   12  C6  UNL     1       0.226   0.046   0.530  1.00  0.00           C  
HETATM   13  C7  UNL     1      -0.749  -0.875   0.207  1.00  0.00           C  
HETATM   14  C8  UNL     1      -1.917  -1.077   1.091  1.00  0.00           C  
HETATM   15  C9  UNL     1      -3.135  -0.422   0.569  1.00  0.00           C  
HETATM   16  C10 UNL     1      -3.323   0.943   0.820  1.00  0.00           C  
HETATM   17  C11 UNL     1      -4.428   1.617   0.376  1.00  0.00           C  
HETATM   18  C12 UNL     1      -5.386   0.942  -0.340  1.00  0.00           C  
HETATM   19  C13 UNL     1      -5.249  -0.391  -0.612  1.00  0.00           C  
HETATM   20  C14 UNL     1      -4.122  -1.056  -0.152  1.00  0.00           C  
HETATM   21  H1  UNL     1       0.584  -1.887  -2.582  1.00  0.00           H  
HETATM   22  H2  UNL     1       2.670   1.868  -0.669  1.00  0.00           H  
HETATM   23  H3  UNL     1       1.701   2.035   0.792  1.00  0.00           H  
HETATM   24  H4  UNL     1       4.834  -0.319   1.488  1.00  0.00           H  
HETATM   25  H5  UNL     1       3.764  -1.036   0.286  1.00  0.00           H  
HETATM   26  H6  UNL     1       4.747   0.586  -1.458  1.00  0.00           H  
HETATM   27  H7  UNL     1       5.920  -0.416  -0.593  1.00  0.00           H  
HETATM   28  H8  UNL     1       6.634   1.164   0.593  1.00  0.00           H  
HETATM   29  H9  UNL     1       0.105   0.597   1.435  1.00  0.00           H  
HETATM   30  H10 UNL     1      -2.129  -2.179   1.194  1.00  0.00           H  
HETATM   31  H11 UNL     1      -1.644  -0.696   2.096  1.00  0.00           H  
HETATM   32  H12 UNL     1      -2.550   1.452   1.390  1.00  0.00           H  
HETATM   33  H13 UNL     1      -4.536   2.658   0.587  1.00  0.00           H  
HETATM   34  H14 UNL     1      -6.281   1.432  -0.715  1.00  0.00           H  
HETATM   35  H15 UNL     1      -5.991  -0.971  -1.181  1.00  0.00           H  
HETATM   36  H16 UNL     1      -4.007  -2.121  -0.358  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3   13
CONECT    3    4   21
CONECT    4    5    5    6
CONECT    6    7   12
CONECT    7    8   22   23
CONECT    8    9
CONECT    9   10   24   25
CONECT   10   11   26   27
CONECT   11   28
CONECT   12   13   13   29
CONECT   13   14
CONECT   14   15   30   31
CONECT   15   16   16   20
CONECT   16   17   32
CONECT   17   18   18   33
CONECT   18   19   34
CONECT   19   20   20   35
CONECT   20   36
END

HMDB0246756
     RDKit          3D
5-Benzylacyclouridine
 36 37  0  0  0  0  0  0  0  0999 V2000
   -1.4798   -2.4392   -1.2745 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6079   -1.5867   -0.9472 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4759   -1.3459   -1.7030 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4198   -0.4282   -1.3540 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3660   -0.3064   -2.1432 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3231    0.2886   -0.2355 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.2881    1.2655    0.1995 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2702    0.8265    1.0190 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1957   -0.0564    0.5901 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1467    0.3968   -0.4634 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8642    1.4933    0.0368 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2262    0.0456    0.5298 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7489   -0.8754    0.2071 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9171   -1.0775    1.0915 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1348   -0.4216    0.5687 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3231    0.9433    0.8204 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4280    1.6171    0.3758 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3860    0.9416   -0.3397 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2490   -0.3909   -0.6116 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1222   -1.0560   -0.1523 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5838   -1.8868   -2.5819 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6703    1.8682   -0.6690 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7015    2.0346    0.7915 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8342   -0.3195    1.4879 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7637   -1.0363    0.2856 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7468    0.5861   -1.4583 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9201   -0.4164   -0.5935 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.6337    1.1638    0.5926 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1053    0.5968    1.4350 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1294   -2.1786    1.1944 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6440   -0.6955    2.0963 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5497    1.4521    1.3896 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5362    2.6579    0.5871 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2811    1.4322   -0.7150 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9912   -0.9712   -1.1806 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0068   -2.1214   -0.3582 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  2  0
  4  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
  6 12  1  0
 12 13  2  0
 13 14  1  0
 14 15  1  0
 15 16  2  0
 16 17  1  0
 17 18  2  0
 18 19  1  0
 19 20  2  0
 13  2  1  0
 20 15  1  0
  3 21  1  0
  7 22  1  0
  7 23  1  0
  9 24  1  0
  9 25  1  0
 10 26  1  0
 10 27  1  0
 11 28  1  0
 12 29  1  0
 14 30  1  0
 14 31  1  0
 16 32  1  0
 17 33  1  0
 18 34  1  0
 19 35  1  0
 20 36  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
BAU	ChEBI
5-Benzyl-1-(2'-hydroxyethoxymethyl)uracil	HMDB
5-BACU	HMDB
5-Benzylacyclouridine	ChEBI

Chemical Formula

C₁₄H₁₆N₂O₄

Average Molecular Weight

276.2878

Monoisotopic Molecular Weight

276.11100701

IUPAC Name

5-benzyl-1-[(2-hydroxyethoxy)methyl]-1,2,3,4-tetrahydropyrimidine-2,4-dione

Traditional Name

5-benzylacyclouridine

CAS Registry Number

Not Available

SMILES

OCCOCN1C=C(CC2=CC=CC=C2)C(=O)NC1=O

InChI Identifier

InChI=1S/C14H16N2O4/c17-6-7-20-10-16-9-12(13(18)15-14(16)19)8-11-4-2-1-3-5-11/h1-5,9,17H,6-8,10H2,(H,15,18,19)

InChI Key

SPJAGILXQBHHSZ-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyrimidones. Pyrimidones are compounds that contain a pyrimidine ring, which bears a ketone. Pyrimidine is a 6-membered ring consisting of four carbon atoms and two nitrogen centers at the 1- and 3- ring positions.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Diazines

Sub Class

Pyrimidines and pyrimidine derivatives

Direct Parent

Pyrimidones

Alternative Parents

Substituents

Pyrimidone
Monocyclic benzene moiety
Hydropyrimidine
Benzenoid
Vinylogous amide
Heteroaromatic compound
Lactam
Urea
Azacycle
Organic oxide
Organopnictogen compound
Primary alcohol
Organooxygen compound
Organonitrogen compound
Alcohol
Organic oxygen compound
Organic nitrogen compound
Hydrocarbon derivative
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

pyrimidone (CHEBI:41037 )
primary alcohol (CHEBI:41037 )
hydroxyether (CHEBI:41037 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 31557052)

Source

Exogenous

Exogenous (HMDB: HMDB0246756)

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	0.48	ALOGPS
logP	0.72	ChemAxon
logS	-2.5	ALOGPS
pKa (Strongest Acidic)	9.95	ChemAxon
pKa (Strongest Basic)	-2.7	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	78.87 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	72.06 m³·mol⁻¹	ChemAxon
Polarizability	28.24 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	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]+	158.881	30932474
DeepCCS	[M-H]-	156.523	30932474
DeepCCS	[M-2H]-	189.409	30932474
DeepCCS	[M+Na]+	164.974	30932474
AllCCS	[M+H]+	161.7	32859911
AllCCS	[M+H-H2O]+	158.1	32859911
AllCCS	[M+NH4]+	165.0	32859911
AllCCS	[M+Na]+	165.9	32859911
AllCCS	[M-H]-	166.0	32859911
AllCCS	[M+Na-2H]-	165.8	32859911
AllCCS	[M+HCOO]-	165.8	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
5-Benzylacyclouridine	OCCOCN1C=C(CC2=CC=CC=C2)C(=O)NC1=O	3754.2	Standard polar	33892256
5-Benzylacyclouridine	OCCOCN1C=C(CC2=CC=CC=C2)C(=O)NC1=O	2365.0	Standard non polar	33892256
5-Benzylacyclouridine	OCCOCN1C=C(CC2=CC=CC=C2)C(=O)NC1=O	2603.1	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
5-Benzylacyclouridine,2TMS,isomer #1	C[Si](C)(C)OCCOCN1C=C(CC2=CC=CC=C2)C(=O)N([Si](C)(C)C)C1=O	2464.0	Semi standard non polar	33892256
5-Benzylacyclouridine,2TMS,isomer #1	C[Si](C)(C)OCCOCN1C=C(CC2=CC=CC=C2)C(=O)N([Si](C)(C)C)C1=O	2637.8	Standard non polar	33892256
5-Benzylacyclouridine,2TMS,isomer #1	C[Si](C)(C)OCCOCN1C=C(CC2=CC=CC=C2)C(=O)N([Si](C)(C)C)C1=O	3030.5	Standard polar	33892256
5-Benzylacyclouridine,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCCOCN1C=C(CC2=CC=CC=C2)C(=O)N([Si](C)(C)C(C)(C)C)C1=O	2924.1	Semi standard non polar	33892256
5-Benzylacyclouridine,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCCOCN1C=C(CC2=CC=CC=C2)C(=O)N([Si](C)(C)C(C)(C)C)C1=O	3017.6	Standard non polar	33892256
5-Benzylacyclouridine,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCCOCN1C=C(CC2=CC=CC=C2)C(=O)N([Si](C)(C)C(C)(C)C)C1=O	3183.8	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Benzylacyclouridine GC-MS (Non-derivatized) - 70eV, Positive	splash10-0gb9-2090000000-590008fedbcf235fd9b7	2017-08-28	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Benzylacyclouridine GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Benzylacyclouridine GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Benzylacyclouridine GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Benzylacyclouridine GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Benzylacyclouridine GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Benzylacyclouridine 10V, Positive-QTOF	splash10-0udi-0190000000-877e6da8219773d3ec64	2017-07-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Benzylacyclouridine 20V, Positive-QTOF	splash10-0udi-0690000000-645a586e8483216c33af	2017-07-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Benzylacyclouridine 40V, Positive-QTOF	splash10-0076-3910000000-292572b45764f9a5313c	2017-07-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Benzylacyclouridine 10V, Negative-QTOF	splash10-003u-5390000000-d14d3f63cb65600b9f06	2017-07-26	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Benzylacyclouridine 20V, Negative-QTOF	splash10-0gvx-9780000000-cd7ac4bb8ba182031f5e	2017-07-26	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Benzylacyclouridine 40V, Negative-QTOF	splash10-0006-9200000000-cd53af3514540a04ea6b	2017-07-26	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Benzylacyclouridine 10V, Positive-QTOF	splash10-00or-0090000000-2243c8c857a717b799bc	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Benzylacyclouridine 20V, Positive-QTOF	splash10-014i-0290000000-fbffbf2b2d98b5e1e010	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Benzylacyclouridine 40V, Positive-QTOF	splash10-00mo-9800000000-a3a6bf66e0275c2916a6	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Benzylacyclouridine 10V, Negative-QTOF	splash10-004i-0090000000-c7ff1c01e4812d0612c7	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Benzylacyclouridine 20V, Negative-QTOF	splash10-0uk9-2590000000-34028d4979d994a0d6ab	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Benzylacyclouridine 40V, Negative-QTOF	splash10-00kf-5900000000-1b9b27f042bf656d02d8	2021-10-12	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

DB07437

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

49600

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

54929

PDB ID

Not Available

ChEBI ID

41037

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 5-Benzylacyclouridine (HMDB0246756)

MOL for HMDB0246756 (5-Benzylacyclouridine)

3D MOL for HMDB0246756 (5-Benzylacyclouridine)

3D SDF for HMDB0246756 (5-Benzylacyclouridine)

3D-SDF for HMDB0246756 (5-Benzylacyclouridine)

PDB for HMDB0246756 (5-Benzylacyclouridine)

3D PDB for HMDB0246756 (5-Benzylacyclouridine)

SMILES for HMDB0246756 (5-Benzylacyclouridine)

INCHI for HMDB0246756 (5-Benzylacyclouridine)

Structure for HMDB0246756 (5-Benzylacyclouridine)

3D Structure for HMDB0246756 (5-Benzylacyclouridine)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra