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Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References enzymes (5) Show 5 proteins XML

Record Information

Version

5.0

Status

Detected and Quantified

Creation Date

2005-11-16 15:48:42 UTC

Update Date

2021-09-14 15:44:40 UTC

HMDB ID

HMDB0000497

Secondary Accession Numbers

HMDB00497

Metabolite Identification

Common Name

5,6-Dihydrouridine

Description

5,6-Dihydrouridine belongs to the class of organic compounds known as glycosylamines. Glycosylamines are compounds consisting of an amine with a beta-N-glycosidic bond to a carbohydrate, thus forming a cyclic hemiaminal ether bond (alpha-amino ether). 5,6-Dihydrouridine has been detected, but not quantified in, a few different foods, such as anatidaes (Anatidae), chickens (Gallus gallus), and domestic pigs (Sus scrofa domestica). This could make 5,6-dihydrouridine a potential biomarker for the consumption of these foods. Based on a literature review a significant number of articles have been published on 5,6-Dihydrouridine.

Structure

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

HMDB0000497
     RDKit          3D
5,6-Dihydrouridine
 31 32  0  0  0  0  0  0  0  0999 V2000
    5.2610   -0.7894   -0.2036 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0220   -0.5992   -0.2399 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5279    0.7982   -0.0617 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3216    0.7192    0.8520 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2960   -0.1611    0.3320 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0492    0.2665    0.3236 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.8908   -0.5262    1.1203 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1258    0.0649    0.8570 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.2207   -0.7893    1.4529 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4734   -0.2591    1.2276 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1554    0.0081   -0.6656 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.0322    0.9355   -1.2059 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7110    0.2994   -1.0192 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.6368    1.5863   -1.5770 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6806   -1.4520   -0.1631 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8214   -2.3570   -0.3345 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0670   -1.6338   -0.4401 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.2630    1.4488    0.4239 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2425    1.2563   -1.0335 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9205    1.7200    1.0522 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7122    0.3456    1.8420 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1216    1.2873    0.7479 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1074    1.0818    1.2484 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0462   -0.8241    2.5501 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0995   -1.8090    1.0258 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5098    0.6163    1.6822 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4469   -1.0365   -0.9197 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8918    0.5179   -1.4237 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2970   -0.3939   -1.7539 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7325    2.2272   -0.8264 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4121   -2.5488   -0.8023 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
  7  8  1  0
  8  9  1  0
  9 10  1  0
  8 11  1  0
 11 12  1  0
 11 13  1  0
 13 14  1  0
  5 15  1  0
 15 16  2  0
 15 17  1  0
 17  2  1  0
 13  6  1  0
  3 18  1  0
  3 19  1  0
  4 20  1  0
  4 21  1  0
  6 22  1  1
  8 23  1  6
  9 24  1  0
  9 25  1  0
 10 26  1  0
 11 27  1  1
 12 28  1  0
 13 29  1  6
 14 30  1  0
 17 31  1  0
M  END


  Mrv0541 02231218332D          

 17 18  0  0  1  0            999 V2000
   18.1059   -6.9732    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.9863   -6.7182    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.5410   -8.4252    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   19.1563   -8.3390    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.4384   -3.1883    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.0095   -5.6633    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.4384   -5.6633    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   16.7240   -4.4257    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   17.4384   -6.4883    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   16.7710   -6.9732    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   17.0259   -7.7577    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   17.8509   -7.7577    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   18.1528   -5.2509    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.1528   -4.4257    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.3359   -8.4252    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.7240   -5.2509    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.4384   -4.0133    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  9  1  0  0  0  0
  1 12  1  0  0  0  0
 10  2  1  1  0  0  0
 11  3  1  1  0  0  0
  4 15  1  0  0  0  0
  5 17  2  0  0  0  0
  6 16  2  0  0  0  0
  9  7  1  6  0  0  0
  7 13  1  0  0  0  0
  7 16  1  0  0  0  0
  8 16  1  0  0  0  0
  8 17  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 15  1  6  0  0  0
 13 14  1  0  0  0  0
 14 17  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0000497

> <DATABASE_NAME>
hmdb

> <SMILES>
OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1CCC(=O)NC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C9H14N2O6/c12-3-4-6(14)7(15)8(17-4)11-2-1-5(13)10-9(11)16/h4,6-8,12,14-15H,1-3H2,(H,10,13,16)/t4-,6-,7-,8-/m1/s1

> <INCHI_KEY>
ZPTBLXKRQACLCR-XVFCMESISA-N

> <FORMULA>
C9H14N2O6

> <MOLECULAR_WEIGHT>
246.2173

> <EXACT_MASS>
246.08518619

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_AVERAGE_POLARIZABILITY>
22.979371465591967

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,3-diazinane-2,4-dione

> <ALOGPS_LOGP>
-2.10

> <JCHEM_LOGP>
-2.773158873

> <ALOGPS_LOGS>
-0.03

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.679741618594914

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.585075095621693

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9802898593286598

> <JCHEM_POLAR_SURFACE_AREA>
119.33

> <JCHEM_REFRACTIVITY>
52.3418

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.31e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
dihydrouridine

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0000497
     RDKit          3D
5,6-Dihydrouridine
 31 32  0  0  0  0  0  0  0  0999 V2000
    5.2610   -0.7894   -0.2036 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0220   -0.5992   -0.2399 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5279    0.7982   -0.0617 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3216    0.7192    0.8520 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2960   -0.1611    0.3320 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0492    0.2665    0.3236 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.8908   -0.5262    1.1203 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1258    0.0649    0.8570 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.2207   -0.7893    1.4529 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4734   -0.2591    1.2276 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1554    0.0081   -0.6656 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.0322    0.9355   -1.2059 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7110    0.2994   -1.0192 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.6368    1.5863   -1.5770 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6806   -1.4520   -0.1631 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8214   -2.3570   -0.3345 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0670   -1.6338   -0.4401 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.2630    1.4488    0.4239 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2425    1.2563   -1.0335 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9205    1.7200    1.0522 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7122    0.3456    1.8420 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1216    1.2873    0.7479 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1074    1.0818    1.2484 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0462   -0.8241    2.5501 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0995   -1.8090    1.0258 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5098    0.6163    1.6822 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4469   -1.0365   -0.9197 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8918    0.5179   -1.4237 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2970   -0.3939   -1.7539 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7325    2.2272   -0.8264 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4121   -2.5488   -0.8023 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
  7  8  1  0
  8  9  1  0
  9 10  1  0
  8 11  1  0
 11 12  1  0
 11 13  1  0
 13 14  1  0
  5 15  1  0
 15 16  2  0
 15 17  1  0
 17  2  1  0
 13  6  1  0
  3 18  1  0
  3 19  1  0
  4 20  1  0
  4 21  1  0
  6 22  1  1
  8 23  1  6
  9 24  1  0
  9 25  1  0
 10 26  1  0
 11 27  1  1
 12 28  1  0
 13 29  1  6
 14 30  1  0
 17 31  1  0
M  END

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  O   UNK     0      33.798 -13.017   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      29.841 -12.541   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      30.877 -15.727   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      35.758 -15.566   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0      32.552  -5.951   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0      29.884 -10.571   0.000  0.00  0.00           O+0
HETATM    7  N   UNK     0      32.552 -10.571   0.000  0.00  0.00           N+0
HETATM    8  N   UNK     0      31.218  -8.261   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0      32.552 -12.111   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      31.306 -13.017   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      31.782 -14.481   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      33.322 -14.481   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      33.885  -9.802   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      33.885  -8.261   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      34.227 -15.727   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      31.218  -9.802   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      32.552  -7.491   0.000  0.00  0.00           C+0
CONECT    1    9   12                                                       
CONECT    2   10                                                            
CONECT    3   11                                                            
CONECT    4   15                                                            
CONECT    5   17                                                            
CONECT    6   16                                                            
CONECT    7    9   13   16                                                  
CONECT    8   16   17                                                       
CONECT    9    1    7   10                                                  
CONECT   10    2    9   11                                                  
CONECT   11    3   10   12                                                  
CONECT   12    1   11   15                                                  
CONECT   13    7   14                                                       
CONECT   14   13   17                                                       
CONECT   15    4   12                                                       
CONECT   16    6    7    8                                                  
CONECT   17    5    8   14                                                  
MASTER        0    0    0    0    0    0    0    0   17    0   36    0
END

COMPND    HMDB0000497
HETATM    1  O1  UNL     1       5.261  -0.789  -0.204  1.00  0.00           O  
HETATM    2  C1  UNL     1       4.022  -0.599  -0.240  1.00  0.00           C  
HETATM    3  C2  UNL     1       3.528   0.798  -0.062  1.00  0.00           C  
HETATM    4  C3  UNL     1       2.322   0.719   0.852  1.00  0.00           C  
HETATM    5  N1  UNL     1       1.296  -0.161   0.332  1.00  0.00           N  
HETATM    6  C4  UNL     1      -0.049   0.267   0.324  1.00  0.00           C  
HETATM    7  O2  UNL     1      -0.891  -0.526   1.120  1.00  0.00           O  
HETATM    8  C5  UNL     1      -2.126   0.065   0.857  1.00  0.00           C  
HETATM    9  C6  UNL     1      -3.221  -0.789   1.453  1.00  0.00           C  
HETATM   10  O3  UNL     1      -4.473  -0.259   1.228  1.00  0.00           O  
HETATM   11  C7  UNL     1      -2.155   0.008  -0.666  1.00  0.00           C  
HETATM   12  O4  UNL     1      -3.032   0.935  -1.206  1.00  0.00           O  
HETATM   13  C8  UNL     1      -0.711   0.299  -1.019  1.00  0.00           C  
HETATM   14  O5  UNL     1      -0.637   1.586  -1.577  1.00  0.00           O  
HETATM   15  C9  UNL     1       1.681  -1.452  -0.163  1.00  0.00           C  
HETATM   16  O6  UNL     1       0.821  -2.357  -0.335  1.00  0.00           O  
HETATM   17  N2  UNL     1       3.067  -1.634  -0.440  1.00  0.00           N  
HETATM   18  H1  UNL     1       4.263   1.449   0.424  1.00  0.00           H  
HETATM   19  H2  UNL     1       3.243   1.256  -1.033  1.00  0.00           H  
HETATM   20  H3  UNL     1       1.920   1.720   1.052  1.00  0.00           H  
HETATM   21  H4  UNL     1       2.712   0.346   1.842  1.00  0.00           H  
HETATM   22  H5  UNL     1      -0.122   1.287   0.748  1.00  0.00           H  
HETATM   23  H6  UNL     1      -2.107   1.082   1.248  1.00  0.00           H  
HETATM   24  H7  UNL     1      -3.046  -0.824   2.550  1.00  0.00           H  
HETATM   25  H8  UNL     1      -3.100  -1.809   1.026  1.00  0.00           H  
HETATM   26  H9  UNL     1      -4.510   0.616   1.682  1.00  0.00           H  
HETATM   27  H10 UNL     1      -2.447  -1.037  -0.920  1.00  0.00           H  
HETATM   28  H11 UNL     1      -3.892   0.518  -1.424  1.00  0.00           H  
HETATM   29  H12 UNL     1      -0.297  -0.394  -1.754  1.00  0.00           H  
HETATM   30  H13 UNL     1      -0.732   2.227  -0.826  1.00  0.00           H  
HETATM   31  H14 UNL     1       3.412  -2.549  -0.802  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3   17
CONECT    3    4   18   19
CONECT    4    5   20   21
CONECT    5    6   15
CONECT    6    7   13   22
CONECT    7    8
CONECT    8    9   11   23
CONECT    9   10   24   25
CONECT   10   26
CONECT   11   12   13   27
CONECT   12   28
CONECT   13   14   29
CONECT   14   30
CONECT   15   16   16   17
CONECT   17   31
END

HMDB0000497
     RDKit          3D
5,6-Dihydrouridine
 31 32  0  0  0  0  0  0  0  0999 V2000
    5.2610   -0.7894   -0.2036 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0220   -0.5992   -0.2399 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5279    0.7982   -0.0617 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3216    0.7192    0.8520 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2960   -0.1611    0.3320 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0492    0.2665    0.3236 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.8908   -0.5262    1.1203 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1258    0.0649    0.8570 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.2207   -0.7893    1.4529 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4734   -0.2591    1.2276 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1554    0.0081   -0.6656 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.0322    0.9355   -1.2059 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7110    0.2994   -1.0192 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.6368    1.5863   -1.5770 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6806   -1.4520   -0.1631 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8214   -2.3570   -0.3345 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0670   -1.6338   -0.4401 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.2630    1.4488    0.4239 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2425    1.2563   -1.0335 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9205    1.7200    1.0522 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7122    0.3456    1.8420 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1216    1.2873    0.7479 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1074    1.0818    1.2484 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0462   -0.8241    2.5501 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0995   -1.8090    1.0258 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5098    0.6163    1.6822 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4469   -1.0365   -0.9197 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8918    0.5179   -1.4237 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2970   -0.3939   -1.7539 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7325    2.2272   -0.8264 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4121   -2.5488   -0.8023 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
  7  8  1  0
  8  9  1  0
  9 10  1  0
  8 11  1  0
 11 12  1  0
 11 13  1  0
 13 14  1  0
  5 15  1  0
 15 16  2  0
 15 17  1  0
 17  2  1  0
 13  6  1  0
  3 18  1  0
  3 19  1  0
  4 20  1  0
  4 21  1  0
  6 22  1  1
  8 23  1  6
  9 24  1  0
  9 25  1  0
 10 26  1  0
 11 27  1  1
 12 28  1  0
 13 29  1  6
 14 30  1  0
 17 31  1  0
M  END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
1-beta-D-Ribofuranosylhydrouracil	ChEBI
3,4-Dihydrouridine	ChEBI
D	ChEBI
1-b-D-Ribofuranosylhydrouracil	Generator
1-Β-D-ribofuranosylhydrouracil	Generator
Dihydro-1-b-D-ribofuranosyl-2,4(1H,3H)-pyrimidinedione	HMDB
Dihydro-1-beta-delta-ribofuranosyl-2,4(1H,3H)-pyrimidinedione	HMDB
Dihydrouridine	HMDB
5,6-Dihydrouridine	MeSH

Chemical Formula

C₉H₁₄N₂O₆

Average Molecular Weight

246.2173

Monoisotopic Molecular Weight

246.08518619

IUPAC Name

1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,3-diazinane-2,4-dione

Traditional Name

dihydrouridine

CAS Registry Number

5627-05-4

SMILES

OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1CCC(=O)NC1=O

InChI Identifier

InChI=1S/C9H14N2O6/c12-3-4-6(14)7(15)8(17-4)11-2-1-5(13)10-9(11)16/h4,6-8,12,14-15H,1-3H2,(H,10,13,16)/t4-,6-,7-,8-/m1/s1

InChI Key

ZPTBLXKRQACLCR-XVFCMESISA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as glycosylamines. Glycosylamines are compounds consisting of an amine with a beta-N-glycosidic bond to a carbohydrate, thus forming a cyclic hemiaminal ether bond (alpha-amino ether).

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Glycosylamines

Alternative Parents

Substituents

N-glycosyl compound
Pentose monosaccharide
Pyrimidone
Hydropyrimidine
1,2,5,6-tetrahydropyrimidine
Monosaccharide
Pyrimidine
Tetrahydrofuran
Secondary alcohol
Carbonic acid derivative
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Oxacycle
Azacycle
Organoheterocyclic compound
Hydrocarbon derivative
Organonitrogen compound
Organopnictogen compound
Carbonyl group
Alcohol
Primary alcohol
Organic nitrogen compound
Organic oxide
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

uridines (CHEBI:23774 )

Ontology

Not Available

Physical Properties

State

Solid

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
Water Solubility	231 g/L	ALOGPS
logP	-2.1	ALOGPS
logP	-2.8	ChemAxon
logS	-0.03	ALOGPS
pKa (Strongest Acidic)	11.59	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	119.33 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	52.34 m³·mol⁻¹	ChemAxon
Polarizability	22.98 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
DarkChem	[M+H]+	155.188	31661259
DarkChem	[M-H]-	151.489	31661259
AllCCS	[M+H]+	155.288	32859911
AllCCS	[M-H]-	153.254	32859911
DeepCCS	[M+H]+	157.562	30932474
DeepCCS	[M-H]-	155.166	30932474
DeepCCS	[M-2H]-	188.051	30932474
DeepCCS	[M+Na]+	163.474	30932474
AllCCS	[M+H]+	155.3	32859911
AllCCS	[M+H-H2O]+	151.6	32859911
AllCCS	[M+NH4]+	158.8	32859911
AllCCS	[M+Na]+	159.7	32859911
AllCCS	[M-H]-	153.3	32859911
AllCCS	[M+Na-2H]-	153.2	32859911
AllCCS	[M+HCOO]-	153.2	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.	1.97 minutes	32390414
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.	2.5 minutes	32390414
Predicted by Siyang on May 30, 2022	10.6986 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	4.87 minutes	32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid	96.9 seconds	40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	1244.1 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	252.7 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	67.8 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	167.8 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	55.9 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	235.0 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	310.5 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	250.1 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	633.0 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	136.0 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	1131.9 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	212.9 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	193.7 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	564.9 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	227.6 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	267.1 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
5,6-Dihydrouridine	OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1CCC(=O)NC1=O	3804.3	Standard polar	33892256
5,6-Dihydrouridine	OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1CCC(=O)NC1=O	2258.7	Standard non polar	33892256
5,6-Dihydrouridine	OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1CCC(=O)NC1=O	2303.8	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
5,6-Dihydrouridine,1TMS,isomer #1	C[Si](C)(C)OC[C@H]1O[C@@H](N2CCC(=O)NC2=O)[C@H](O)[C@@H]1O	2294.7	Semi standard non polar	33892256
5,6-Dihydrouridine,1TMS,isomer #2	C[Si](C)(C)O[C@@H]1[C@H](O)[C@@H](CO)O[C@H]1N1CCC(=O)NC1=O	2321.5	Semi standard non polar	33892256
5,6-Dihydrouridine,1TMS,isomer #3	C[Si](C)(C)O[C@@H]1[C@@H](CO)O[C@@H](N2CCC(=O)NC2=O)[C@@H]1O	2318.6	Semi standard non polar	33892256
5,6-Dihydrouridine,1TMS,isomer #4	C[Si](C)(C)N1C(=O)CCN([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)C1=O	2265.9	Semi standard non polar	33892256
5,6-Dihydrouridine,2TMS,isomer #1	C[Si](C)(C)OC[C@H]1O[C@@H](N2CCC(=O)NC2=O)[C@H](O[Si](C)(C)C)[C@@H]1O	2350.5	Semi standard non polar	33892256
5,6-Dihydrouridine,2TMS,isomer #2	C[Si](C)(C)OC[C@H]1O[C@@H](N2CCC(=O)NC2=O)[C@H](O)[C@@H]1O[Si](C)(C)C	2336.1	Semi standard non polar	33892256
5,6-Dihydrouridine,2TMS,isomer #3	C[Si](C)(C)OC[C@H]1O[C@@H](N2CCC(=O)N([Si](C)(C)C)C2=O)[C@H](O)[C@@H]1O	2272.9	Semi standard non polar	33892256
5,6-Dihydrouridine,2TMS,isomer #4	C[Si](C)(C)O[C@@H]1[C@@H](CO)O[C@@H](N2CCC(=O)NC2=O)[C@@H]1O[Si](C)(C)C	2347.9	Semi standard non polar	33892256
5,6-Dihydrouridine,2TMS,isomer #5	C[Si](C)(C)O[C@@H]1[C@H](O)[C@@H](CO)O[C@H]1N1CCC(=O)N([Si](C)(C)C)C1=O	2245.3	Semi standard non polar	33892256
5,6-Dihydrouridine,2TMS,isomer #6	C[Si](C)(C)O[C@@H]1[C@@H](CO)O[C@@H](N2CCC(=O)N([Si](C)(C)C)C2=O)[C@@H]1O	2258.4	Semi standard non polar	33892256
5,6-Dihydrouridine,3TMS,isomer #1	C[Si](C)(C)OC[C@H]1O[C@@H](N2CCC(=O)NC2=O)[C@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C	2350.1	Semi standard non polar	33892256
5,6-Dihydrouridine,3TMS,isomer #2	C[Si](C)(C)OC[C@H]1O[C@@H](N2CCC(=O)N([Si](C)(C)C)C2=O)[C@H](O[Si](C)(C)C)[C@@H]1O	2279.2	Semi standard non polar	33892256
5,6-Dihydrouridine,3TMS,isomer #3	C[Si](C)(C)OC[C@H]1O[C@@H](N2CCC(=O)N([Si](C)(C)C)C2=O)[C@H](O)[C@@H]1O[Si](C)(C)C	2270.4	Semi standard non polar	33892256
5,6-Dihydrouridine,3TMS,isomer #4	C[Si](C)(C)O[C@@H]1[C@@H](CO)O[C@@H](N2CCC(=O)N([Si](C)(C)C)C2=O)[C@@H]1O[Si](C)(C)C	2258.5	Semi standard non polar	33892256
5,6-Dihydrouridine,4TMS,isomer #1	C[Si](C)(C)OC[C@H]1O[C@@H](N2CCC(=O)N([Si](C)(C)C)C2=O)[C@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C	2286.8	Semi standard non polar	33892256
5,6-Dihydrouridine,4TMS,isomer #1	C[Si](C)(C)OC[C@H]1O[C@@H](N2CCC(=O)N([Si](C)(C)C)C2=O)[C@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C	2470.2	Standard non polar	33892256
5,6-Dihydrouridine,4TMS,isomer #1	C[Si](C)(C)OC[C@H]1O[C@@H](N2CCC(=O)N([Si](C)(C)C)C2=O)[C@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C	2772.9	Standard polar	33892256
5,6-Dihydrouridine,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2CCC(=O)NC2=O)[C@H](O)[C@@H]1O	2532.6	Semi standard non polar	33892256
5,6-Dihydrouridine,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)O[C@@H]1[C@H](O)[C@@H](CO)O[C@H]1N1CCC(=O)NC1=O	2543.3	Semi standard non polar	33892256
5,6-Dihydrouridine,1TBDMS,isomer #3	CC(C)(C)[Si](C)(C)O[C@@H]1[C@@H](CO)O[C@@H](N2CCC(=O)NC2=O)[C@@H]1O	2536.7	Semi standard non polar	33892256
5,6-Dihydrouridine,1TBDMS,isomer #4	CC(C)(C)[Si](C)(C)N1C(=O)CCN([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)C1=O	2503.0	Semi standard non polar	33892256
5,6-Dihydrouridine,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2CCC(=O)NC2=O)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O	2767.9	Semi standard non polar	33892256
5,6-Dihydrouridine,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2CCC(=O)NC2=O)[C@H](O)[C@@H]1O[Si](C)(C)C(C)(C)C	2753.5	Semi standard non polar	33892256
5,6-Dihydrouridine,2TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2CCC(=O)N([Si](C)(C)C(C)(C)C)C2=O)[C@H](O)[C@@H]1O	2708.1	Semi standard non polar	33892256
5,6-Dihydrouridine,2TBDMS,isomer #4	CC(C)(C)[Si](C)(C)O[C@@H]1[C@@H](CO)O[C@@H](N2CCC(=O)NC2=O)[C@@H]1O[Si](C)(C)C(C)(C)C	2748.6	Semi standard non polar	33892256
5,6-Dihydrouridine,2TBDMS,isomer #5	CC(C)(C)[Si](C)(C)O[C@@H]1[C@H](O)[C@@H](CO)O[C@H]1N1CCC(=O)N([Si](C)(C)C(C)(C)C)C1=O	2699.9	Semi standard non polar	33892256
5,6-Dihydrouridine,2TBDMS,isomer #6	CC(C)(C)[Si](C)(C)O[C@@H]1[C@@H](CO)O[C@@H](N2CCC(=O)N([Si](C)(C)C(C)(C)C)C2=O)[C@@H]1O	2702.9	Semi standard non polar	33892256
5,6-Dihydrouridine,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2CCC(=O)NC2=O)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O[Si](C)(C)C(C)(C)C	3004.3	Semi standard non polar	33892256
5,6-Dihydrouridine,3TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2CCC(=O)N([Si](C)(C)C(C)(C)C)C2=O)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O	2940.8	Semi standard non polar	33892256
5,6-Dihydrouridine,3TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2CCC(=O)N([Si](C)(C)C(C)(C)C)C2=O)[C@H](O)[C@@H]1O[Si](C)(C)C(C)(C)C	2935.0	Semi standard non polar	33892256
5,6-Dihydrouridine,3TBDMS,isomer #4	CC(C)(C)[Si](C)(C)O[C@@H]1[C@@H](CO)O[C@@H](N2CCC(=O)N([Si](C)(C)C(C)(C)C)C2=O)[C@@H]1O[Si](C)(C)C(C)(C)C	2921.7	Semi standard non polar	33892256
5,6-Dihydrouridine,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2CCC(=O)N([Si](C)(C)C(C)(C)C)C2=O)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O[Si](C)(C)C(C)(C)C	3155.4	Semi standard non polar	33892256
5,6-Dihydrouridine,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2CCC(=O)N([Si](C)(C)C(C)(C)C)C2=O)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O[Si](C)(C)C(C)(C)C	3323.9	Standard non polar	33892256
5,6-Dihydrouridine,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2CCC(=O)N([Si](C)(C)C(C)(C)C)C2=O)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O[Si](C)(C)C(C)(C)C	3101.4	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - 5,6-Dihydrouridine GC-MS (Non-derivatized) - 70eV, Positive	splash10-0a4i-9630000000-15e433fd50f5283e7c70	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5,6-Dihydrouridine GC-MS (3 TMS) - 70eV, Positive	splash10-0fa2-5977600000-2e6dc8e47acc572f91e7	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5,6-Dihydrouridine GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5,6-Dihydrouridine GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5,6-Dihydrouridine GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5,6-Dihydrouridine GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5,6-Dihydrouridine GC-MS (TMS_1_3) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5,6-Dihydrouridine GC-MS (TMS_1_4) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5,6-Dihydrouridine GC-MS (TMS_2_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5,6-Dihydrouridine GC-MS (TMS_2_2) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5,6-Dihydrouridine GC-MS (TMS_2_3) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5,6-Dihydrouridine GC-MS (TMS_2_4) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5,6-Dihydrouridine GC-MS (TMS_2_5) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5,6-Dihydrouridine GC-MS (TMS_2_6) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5,6-Dihydrouridine GC-MS (TMS_3_2) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5,6-Dihydrouridine GC-MS (TMS_3_3) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5,6-Dihydrouridine GC-MS (TMS_3_4) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5,6-Dihydrouridine GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5,6-Dihydrouridine GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5,6-Dihydrouridine GC-MS (TBDMS_1_3) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5,6-Dihydrouridine GC-MS (TBDMS_1_4) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5,6-Dihydrouridine GC-MS (TBDMS_2_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5,6-Dihydrouridine GC-MS (TBDMS_2_2) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5,6-Dihydrouridine GC-MS (TBDMS_2_3) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5,6-Dihydrouridine GC-MS (TBDMS_2_4) - 70eV, Positive	Not Available	2021-11-05	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 - 5,6-Dihydrouridine 10V, Positive-QTOF	splash10-014i-1920000000-6709bfe12a99399905ae	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5,6-Dihydrouridine 20V, Positive-QTOF	splash10-014i-8900000000-8c868a51dd1b65e8911f	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5,6-Dihydrouridine 40V, Positive-QTOF	splash10-014m-9500000000-65ec5beb0c86d7c307b3	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5,6-Dihydrouridine 10V, Negative-QTOF	splash10-01ot-2690000000-33fe0d39759c16898235	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5,6-Dihydrouridine 20V, Negative-QTOF	splash10-0006-9100000000-bb26ee994aafc4e96a2e	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5,6-Dihydrouridine 40V, Negative-QTOF	splash10-0006-9100000000-4c20e49ada219697c154	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5,6-Dihydrouridine 10V, Positive-QTOF	splash10-014i-0920000000-4ef817592c10e76e901d	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5,6-Dihydrouridine 20V, Positive-QTOF	splash10-014i-2920000000-e1ff0efd002a4870b8d2	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5,6-Dihydrouridine 40V, Positive-QTOF	splash10-01b9-9700000000-c671b5ded8fa9d4e6734	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5,6-Dihydrouridine 10V, Negative-QTOF	splash10-01r2-0590000000-4d20d79523dcba08b44a	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5,6-Dihydrouridine 20V, Negative-QTOF	splash10-0hfw-4940000000-4e7d076c3dc715e35ccf	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5,6-Dihydrouridine 40V, Negative-QTOF	splash10-0006-9200000000-d9747b2acc3e65b6ad8c	2021-09-23	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm

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 Available	Not Available	Normal	Not Available	details
Urine	Detected and Quantified	7.03 +/- 1.31 umol/mmol creatinine	Adult (>18 years old)	Female	Normal	9129323	details
Urine	Detected and Quantified	5.83 +/- 1.22 umol/mmol creatinine	Adult (>18 years old)	Male	Normal	9129323	details
Urine	Detected and Quantified	6.37 +/- 1.38 umol/mmol creatinine	Adult (>18 years old)	Both	Normal	9129323	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

FDB022076

KNApSAcK ID

Not Available

Chemspider ID

85115

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Dihydrouridine

METLIN ID

5483

PubChem Compound

94312

PDB ID

Not Available

ChEBI ID

23774

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Cerutti, Peter; Kondo, Yoshikazu; Landis, W. R.; Witkop, Bernhard. Photoreduction of uridine and reduction of dihydrouridine with sodium borohydride. Journal of the American Chemical Society (1968), 90(3), 771-5.

Material Safety Data Sheet (MSDS)

Not Available

General References

Liebich HM, Di Stefano C, Wixforth A, Schmid HR: Quantitation of urinary nucleosides by high-performance liquid chromatography. J Chromatogr A. 1997 Feb 28;763(1-2):193-7. [PubMed:9129323 ]
Reimer ML, Schram KH, Nakano K, Yasaka T: The identification of 5,6-dihydrouridine in normal human urine by combined gas chromatography/mass spectrometry. Anal Biochem. 1989 Sep;181(2):302-8. [PubMed:2817393 ]
Topp H, Duden R, Schoch G: 5,6-Dihydrouridine: a marker ribonucleoside for determining whole body degradation rates of transfer RNA in man and rats. Clin Chim Acta. 1993 Sep 17;218(1):73-82. [PubMed:8299222 ]

Enzymes

Enzyme Details

1. tRNA-dihydrouridine synthase 2-like

General function:: Involved in catalytic activity
Specific function:: Dihydrouridine synthase. Catalyzes the synthesis of dihydrouridine, a modified base found in the D-loop of most tRNAs
Gene Name:: DUS2L
Uniprot ID:: Q9NX74
Molecular weight:: 55049.8

Enzyme Details

2. tRNA-dihydrouridine synthase 1-like

General function:: Involved in catalytic activity
Specific function:: Catalyzes the synthesis of dihydrouridine, a modified base found in the D-loop of most tRNAs
Gene Name:: DUS1L
Uniprot ID:: Q6P1R4
Molecular weight:: 53230.0

Enzyme Details

3. tRNA-dihydrouridine synthase 3-like

General function:: Involved in catalytic activity
Specific function:: Catalyzes the synthesis of dihydrouridine, a modified base found in the D-loop of most tRNAs
Gene Name:: DUS3L
Uniprot ID:: Q96G46
Molecular weight:: 72593.3

Enzyme Details

4. tRNA-dihydrouridine synthase 4-like

General function:: Involved in catalytic activity
Specific function:: Catalyzes the synthesis of dihydrouridine, a modified base found in the D-loop of most tRNAs
Gene Name:: DUS4L
Uniprot ID:: O95620
Molecular weight:: 35816.2

Enzyme Details

5. Dihydrouridine synthase 4-like (S. cerevisiae), isoform CRA_c

General function:: Involved in catalytic activity
Specific function:: Not Available
Gene Name:: PP35
Uniprot ID:: A4D0R5
Molecular weight:: 35816.2

Showing metabocard for 5,6-Dihydrouridine (HMDB0000497)

MOL for HMDB0000497 (5,6-Dihydrouridine)

3D MOL for HMDB0000497 (5,6-Dihydrouridine)

3D SDF for HMDB0000497 (5,6-Dihydrouridine)

3D-SDF for HMDB0000497 (5,6-Dihydrouridine)

PDB for HMDB0000497 (5,6-Dihydrouridine)

3D PDB for HMDB0000497 (5,6-Dihydrouridine)

SMILES for HMDB0000497 (5,6-Dihydrouridine)

INCHI for HMDB0000497 (5,6-Dihydrouridine)

Structure for HMDB0000497 (5,6-Dihydrouridine)

3D Structure for HMDB0000497 (5,6-Dihydrouridine)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

Enzymes