MiMeDB: Showing metabocard for Uridine (MMDBc0000094)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2020-10-27 23:30:09 UTC

Update Date

2022-08-30 23:34:00 UTC

Metabolite ID

MMDBc0000094

Metabolite Identification

Common Name

Uridine

Description

Uridine, also known as beta-uridine or 1-beta-D-ribofuranosylpyrimidine-2,4(1H,3H)-dione, is a member of the class of compounds known as pyrimidine nucleosides. Pyrimidine nucleosides are compounds comprising a pyrimidine base attached to a ribosyl or deoxyribosyl moiety. More specifically, uridine is a nucleoside consisting of uracil and D-ribose and a component of RNA. Uridine is soluble (in water) and a very weakly acidic compound (based on its pKa). Uridine can be synthesized from uracil. It is one of the five standard nucleosides which make up nucleic acids, the others being adenosine, thymidine, cytidine and guanosine. The five nucleosides are commonly abbreviated to their one-letter codes U, A, T, C and G respectively. Uridine is also a parent compound for other transformation products, including but not limited to, nikkomycin Z, 3'-(enolpyruvyl)uridine 5'-monophosphate, and 5-aminomethyl-2-thiouridine. Uridine can be found in most biofluids, including urine, breast milk, cerebrospinal fluid (CSF), and blood. Within the cell, uridine is primarily located in the mitochondria, in the nucleus and the lysosome. It can also be found in the extracellular space. As an essential nucleoside, uridine exists in all living species, ranging from bacteria to humans. In humans, uridine is involved in several metabolic disorders, some of which include dhydropyrimidinase deficiency, MNGIE (mitochondrial neurogastrointestinal encephalopathy), and beta-ureidopropionase deficiency. Moreover, uridine is found to be associated with Lesch-Nyhan syndrome, which is an inborn error of metabolism. Uridine is a nucleoside consisting of uracil and D-ribose and a component of RNA. Uridine plays a role in the glycolysis pathway of galactose. In humans there is no catabolic process to metabolize galactose. Therefore, galactose is converted to glucose and metabolized via the normal glucose metabolism pathways. More specifically, consumed galactose is converted into galactose 1-phosphate (Gal-1-P). This molecule is a substrate for the enzyme galactose-1-phosphate uridyl transferase which transfers a UDP molecule to the galactose molecule. The end result is UDP-galactose and glucose-1-phosphate. This process is continued to allow the proper glycolysis of galactose. Uridine is found in many foods (anything containing RNA) but is destroyed in the liver and gastrointestinal tract, and so no food, when consumed, has ever been reliably shown to elevate blood uridine levels. On the other hand, consumption of RNA-rich foods may lead to high levels of purines (adenine and guanosine) in blood. High levels of purines are known to increase uric acid production and may aggravate or lead to conditions such as gout.

Structure

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

HMDB0000296
     RDKit          3D
Uridine
 29 30  0  0  0  0  0  0  0  0999 V2000
    5.4528   -0.1646   -0.5518 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2120   -0.1635   -0.3987 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6593    0.4277    0.7081 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3025    0.4143    0.8501 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4700   -0.1577   -0.0541 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0766   -0.1078    0.2036 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.6830   -1.0635   -0.4136 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9724   -0.6966   -0.0001 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.0343   -1.3987   -0.8142 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2709   -0.9718   -0.3319 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0554    0.8003   -0.1185 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.4537    1.3579    1.1004 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5790    1.1840   -0.2854 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.2267    2.2216    0.5490 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0411   -0.7283   -1.1270 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2511   -1.2604   -1.9661 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3751   -0.7289   -1.2907 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.2741    0.9060    1.4741 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8871    0.8881    1.7336 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1455   -0.1454    1.3031 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0346   -0.9755    1.0714 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9060   -1.2308   -1.8876 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9574   -2.4912   -0.5422 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2502   -0.8541    0.6336 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6675    1.1341   -0.9584 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2495    0.7100    1.8330 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3744    1.3628   -1.3517 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9402    2.9056    0.6483 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7992   -1.1736   -2.1243 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  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
  4 19  1  0
  6 20  1  1
  8 21  1  1
  9 22  1  0
  9 23  1  0
 10 24  1  0
 11 25  1  6
 12 26  1  0
 13 27  1  6
 14 28  1  0
 17 29  1  0
M  END


  Mrv1652309042000002D          

 17 18  0  0  1  0            999 V2000
    0.0000   -0.8250    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6674   -1.3099    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6675   -1.3099    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7145    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7144    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -2.0945    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.4125   -2.0945    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4521   -1.0550    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2374    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4290    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7144    1.2374    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8975   -2.7620    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8974   -2.7620    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5618   -3.5157    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    2.4749    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  1  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  0  0  0
  2  5  1  0  0  0  0
  2  6  1  0  0  0  0
  3  7  1  0  0  0  0
  4  8  1  0  0  0  0
  4  9  1  6  0  0  0
  5 10  1  0  0  0  0
  5 11  2  0  0  0  0
  6 12  2  0  0  0  0
  7 15  1  1  0  0  0
  8 13  1  6  0  0  0
 10 14  1  0  0  0  0
 14 17  2  0  0  0  0
  7  8  1  0  0  0  0
 12 14  1  0  0  0  0
 15 16  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0000094

> <DATABASE_NAME>
MIME

> <SMILES>
OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C=CC(=O)NC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C9H12N2O6/c12-3-4-6(14)7(15)8(17-4)11-2-1-5(13)10-9(11)16/h1-2,4,6-8,12,14-15H,3H2,(H,10,13,16)/t4-,6-,7-,8-/m1/s1

> <INCHI_KEY>
DRTQHJPVMGBUCF-XVFCMESISA-N

> <FORMULA>
C9H12N2O6

> <MOLECULAR_WEIGHT>
244.2014

> <EXACT_MASS>
244.069536126

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
29

> <JCHEM_AVERAGE_POLARIZABILITY>
21.809000940587058

> <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]-1,2,3,4-tetrahydropyrimidine-2,4-dione

> <ALOGPS_LOGP>
-1.84

> <JCHEM_LOGP>
-2.415242141666667

> <ALOGPS_LOGS>
-0.26

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.620123384629313

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.700740441527786

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9802996389517045

> <JCHEM_POLAR_SURFACE_AREA>
119.32999999999998

> <JCHEM_REFRACTIVITY>
52.56559999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.35e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
uridine

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0000296
     RDKit          3D
Uridine
 29 30  0  0  0  0  0  0  0  0999 V2000
    5.4528   -0.1646   -0.5518 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2120   -0.1635   -0.3987 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6593    0.4277    0.7081 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3025    0.4143    0.8501 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4700   -0.1577   -0.0541 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0766   -0.1078    0.2036 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.6830   -1.0635   -0.4136 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9724   -0.6966   -0.0001 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.0343   -1.3987   -0.8142 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2709   -0.9718   -0.3319 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0554    0.8003   -0.1185 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.4537    1.3579    1.1004 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5790    1.1840   -0.2854 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.2267    2.2216    0.5490 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0411   -0.7283   -1.1270 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2511   -1.2604   -1.9661 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3751   -0.7289   -1.2907 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.2741    0.9060    1.4741 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8871    0.8881    1.7336 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1455   -0.1454    1.3031 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0346   -0.9755    1.0714 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9060   -1.2308   -1.8876 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9574   -2.4912   -0.5422 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2502   -0.8541    0.6336 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6675    1.1341   -0.9584 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2495    0.7100    1.8330 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3744    1.3628   -1.3517 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9402    2.9056    0.6483 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7992   -1.1736   -2.1243 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  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
  4 19  1  0
  6 20  1  1
  8 21  1  1
  9 22  1  0
  9 23  1  0
 10 24  1  0
 11 25  1  6
 12 26  1  0
 13 27  1  6
 14 28  1  0
 17 29  1  0
M  END

HEADER    PROTEIN                                 04-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-20         0                                  
HETATM    1  C   UNK     0       0.000  -1.540   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM    3  O   UNK     0      -1.246  -2.445   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       1.246  -2.445   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.334   0.770   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -1.334   0.770   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -0.770  -3.910   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.770  -3.910   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       2.711  -1.969   0.000  0.00  0.00           O+0
HETATM   10  N   UNK     0       1.334   2.310   0.000  0.00  0.00           N+0
HETATM   11  O   UNK     0       2.667   0.000   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      -1.334   2.310   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       1.675  -5.156   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       0.000   3.080   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -1.675  -5.156   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      -1.049  -6.563   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       0.000   4.620   0.000  0.00  0.00           O+0
CONECT    1    2    3    4                                                  
CONECT    2    1    5    6                                                  
CONECT    3    1    7                                                       
CONECT    4    1    8    9                                                  
CONECT    5    2   10   11                                                  
CONECT    6    2   12                                                       
CONECT    7    3   15    8                                                  
CONECT    8    4   13    7                                                  
CONECT    9    4                                                            
CONECT   10    5   14                                                       
CONECT   11    5                                                            
CONECT   12    6   14                                                       
CONECT   13    8                                                            
CONECT   14   10   17   12                                                  
CONECT   15    7   16                                                       
CONECT   16   15                                                            
CONECT   17   14                                                            
MASTER        0    0    0    0    0    0    0    0   17    0   36    0
END

COMPND    HMDB0000296
HETATM    1  O1  UNL     1       5.453  -0.165  -0.552  1.00  0.00           O  
HETATM    2  C1  UNL     1       4.212  -0.164  -0.399  1.00  0.00           C  
HETATM    3  C2  UNL     1       3.659   0.428   0.708  1.00  0.00           C  
HETATM    4  C3  UNL     1       2.302   0.414   0.850  1.00  0.00           C  
HETATM    5  N1  UNL     1       1.470  -0.158  -0.054  1.00  0.00           N  
HETATM    6  C4  UNL     1       0.077  -0.108   0.204  1.00  0.00           C  
HETATM    7  O2  UNL     1      -0.683  -1.063  -0.414  1.00  0.00           O  
HETATM    8  C5  UNL     1      -1.972  -0.697  -0.000  1.00  0.00           C  
HETATM    9  C6  UNL     1      -3.034  -1.399  -0.814  1.00  0.00           C  
HETATM   10  O3  UNL     1      -4.271  -0.972  -0.332  1.00  0.00           O  
HETATM   11  C7  UNL     1      -2.055   0.800  -0.118  1.00  0.00           C  
HETATM   12  O4  UNL     1      -2.454   1.358   1.100  1.00  0.00           O  
HETATM   13  C8  UNL     1      -0.579   1.184  -0.285  1.00  0.00           C  
HETATM   14  O5  UNL     1      -0.227   2.222   0.549  1.00  0.00           O  
HETATM   15  C9  UNL     1       2.041  -0.728  -1.127  1.00  0.00           C  
HETATM   16  O6  UNL     1       1.251  -1.260  -1.966  1.00  0.00           O  
HETATM   17  N2  UNL     1       3.375  -0.729  -1.291  1.00  0.00           N  
HETATM   18  H1  UNL     1       4.274   0.906   1.474  1.00  0.00           H  
HETATM   19  H2  UNL     1       1.887   0.888   1.734  1.00  0.00           H  
HETATM   20  H3  UNL     1      -0.146  -0.145   1.303  1.00  0.00           H  
HETATM   21  H4  UNL     1      -2.035  -0.975   1.071  1.00  0.00           H  
HETATM   22  H5  UNL     1      -2.906  -1.231  -1.888  1.00  0.00           H  
HETATM   23  H6  UNL     1      -2.957  -2.491  -0.542  1.00  0.00           H  
HETATM   24  H7  UNL     1      -4.250  -0.854   0.634  1.00  0.00           H  
HETATM   25  H8  UNL     1      -2.668   1.134  -0.958  1.00  0.00           H  
HETATM   26  H9  UNL     1      -2.249   0.710   1.833  1.00  0.00           H  
HETATM   27  H10 UNL     1      -0.374   1.363  -1.352  1.00  0.00           H  
HETATM   28  H11 UNL     1      -0.940   2.906   0.648  1.00  0.00           H  
HETATM   29  H12 UNL     1       3.799  -1.174  -2.124  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3   17
CONECT    3    4    4   18
CONECT    4    5   19
CONECT    5    6   15
CONECT    6    7   13   20
CONECT    7    8
CONECT    8    9   11   21
CONECT    9   10   22   23
CONECT   10   24
CONECT   11   12   13   25
CONECT   12   26
CONECT   13   14   27
CONECT   14   28
CONECT   15   16   16   17
CONECT   17   29
END

HMDB0000296
     RDKit          3D
Uridine
 29 30  0  0  0  0  0  0  0  0999 V2000
    5.4528   -0.1646   -0.5518 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2120   -0.1635   -0.3987 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6593    0.4277    0.7081 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3025    0.4143    0.8501 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4700   -0.1577   -0.0541 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0766   -0.1078    0.2036 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.6830   -1.0635   -0.4136 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9724   -0.6966   -0.0001 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.0343   -1.3987   -0.8142 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2709   -0.9718   -0.3319 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0554    0.8003   -0.1185 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.4537    1.3579    1.1004 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5790    1.1840   -0.2854 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.2267    2.2216    0.5490 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0411   -0.7283   -1.1270 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2511   -1.2604   -1.9661 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3751   -0.7289   -1.2907 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.2741    0.9060    1.4741 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8871    0.8881    1.7336 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1455   -0.1454    1.3031 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0346   -0.9755    1.0714 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9060   -1.2308   -1.8876 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9574   -2.4912   -0.5422 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2502   -0.8541    0.6336 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6675    1.1341   -0.9584 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2495    0.7100    1.8330 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3744    1.3628   -1.3517 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9402    2.9056    0.6483 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7992   -1.1736   -2.1243 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  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
  4 19  1  0
  6 20  1  1
  8 21  1  1
  9 22  1  0
  9 23  1  0
 10 24  1  0
 11 25  1  6
 12 26  1  0
 13 27  1  6
 14 28  1  0
 17 29  1  0
M  END

Synonyms

Value	Source
1-beta-D-Ribofuranosylpyrimidine-2,4(1H,3H)-dione	ChEBI
1-beta-D-Ribofuranosyluracil	ChEBI
beta-Uridine	ChEBI
u	ChEBI
Urd	ChEBI
Uridin	ChEBI
1-b-D-Ribofuranosylpyrimidine-2,4(1H,3H)-dione	Generator
1-Β-D-ribofuranosylpyrimidine-2,4(1H,3H)-dione	Generator
1-b-D-Ribofuranosyluracil	Generator
1-Β-D-ribofuranosyluracil	Generator
b-Uridine	Generator
Β-uridine	Generator
1-b-D-Ribofuranosyl-2,4(1H,3H)-pyrimidinedione	HMDB
1-beta-delta-Ribofuranosyl-2,4(1H,3H)-pyrimidinedione	HMDB
1-beta-delta-Ribofuranosyluracil	HMDB
b-D-Ribofuranoside 2,4(1H,3H)-pyrimidinedione-1	HMDB
beta-delta-Ribofuranoside 2,4(1H,3H)-pyrimidinedione-1	HMDB
Allo uridine	HMDB
Allo-uridine	HMDB
Allouridine	HMDB

Molecular Formula

C₉H₁₂N₂O₆

Average Mass

244.2014

Monoisotopic Mass

244.069536126

IUPAC Name

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

Traditional Name

uridine

CAS Registry Number

58-96-8

SMILES

OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C=CC(=O)NC1=O

InChI Identifier

InChI=1S/C9H12N2O6/c12-3-4-6(14)7(15)8(17-4)11-2-1-5(13)10-9(11)16/h1-2,4,6-8,12,14-15H,3H2,(H,10,13,16)/t4-,6-,7-,8-/m1/s1

InChI Key

DRTQHJPVMGBUCF-XVFCMESISA-N

Chemical Taxonomy

Description

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

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Pyrimidine nucleosides

Sub Class

Not Available

Direct Parent

Pyrimidine nucleosides

Alternative Parents

Substituents

Pyrimidine nucleoside
Glycosyl compound
N-glycosyl compound
Pentose monosaccharide
Pyrimidone
Hydropyrimidine
Monosaccharide
Pyrimidine
Vinylogous amide
Tetrahydrofuran
Heteroaromatic compound
Urea
Secondary alcohol
Lactam
Organoheterocyclic compound
Oxacycle
Azacycle
Hydrocarbon derivative
Organopnictogen compound
Organooxygen compound
Organonitrogen compound
Primary alcohol
Alcohol
Organic oxygen compound
Organic oxide
Organic nitrogen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

uridines (CHEBI:16704 )
Ribonucleosides (C00299 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	135 g/L	ALOGPS
logP	-1.8	ALOGPS
logP	-2.4	ChemAxon
logS	-0.26	ALOGPS
pKa (Strongest Acidic)	9.7	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	52.57 m³·mol⁻¹	ChemAxon
Polarizability	21.81 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

Spectra

Chromatographic Retention Times and Retention Indices

Retention Times

Not Available

Retention Indices

Not Available

Chromatographic Retention Times and Retention Indices

Retention Times

Not Available

Retention Indices

Not Available

Biological Properties

Cellular Locations

Extracellular
Lysosome
Mitochondria
Nucleus

Biospecimen Locations

Blood
Breast Milk
Cerebrospinal Fluid (CSF)
Feces
Placenta
Urine

Tissue Locations

Placenta

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species
MMDBp0191677	5'-nucleotidase	Unknown	P21589	Homo_sapiens
MMDBp0191680	Cytosolic 5'-nucleotidase 1B	Unknown	Q96P26	Homo_sapiens
MMDBp0191681	Cytosolic 5'-nucleotidase 1A	Unknown	Q9BXI3	Homo_sapiens
MMDBp0191682	5'(3')-deoxyribonucleotidase, cytosolic type	Unknown	Q8TCD5	Homo_sapiens
MMDBp0191684	5'(3')-deoxyribonucleotidase, mitochondrial	Unknown	Q9NPB1	Homo_sapiens
MMDBp0191778	Uridine-cytidine kinase 1	Unknown	Q9HA47	Homo_sapiens
MMDBp0192704	tRNA pseudouridine synthase A, mitochondrial	Enzyme	Q9Y606	Homo_sapiens
MMDBp0193196	H/ACA ribonucleoprotein complex subunit 4	Enzyme	O60832	Homo_sapiens
MMDBp0193590	Uridine-cytidine kinase 2	Unknown	Q9BZX2	Homo_sapiens
MMDBp0193783	AID	Enzyme	Q546Y9	Homo_sapiens
MMDBp0193860	Cytosolic 5'-nucleotidase 3	Enzyme	Q9H0P0	Homo_sapiens
MMDBp0193932	Cytosolic purine 5'-nucleotidase	Unknown	P49902	Homo_sapiens
MMDBp0194012	Cytidine deaminase	Unknown	P32320	Homo_sapiens
MMDBp0194034	Uridine phosphorylase 1	Enzyme	Q16831	Homo_sapiens
MMDBp0194035	Uridine phosphorylase 2	Enzyme	O95045	Homo_sapiens
MMDBp0194185	Uridine-cytidine kinase-like 1	Enzyme	Q9NWZ5	Homo_sapiens
MMDBp0195902	Putative tRNA pseudouridine synthase Pus10	Enzyme	Q3MIT2	Homo_sapiens
MMDBp0195903	tRNA pseudouridine synthase 3	Enzyme	Q9BZE2	Homo_sapiens
MMDBp0196233	tRNA pseudouridine synthase-like 1	Enzyme	Q8N0Z8	Homo_sapiens
MMDBp0196270	DNA dC->dU-editing enzyme APOBEC-3H	Enzyme	Q6NTF7	Homo_sapiens
MMDBp0196667	Probable DNA dC->dU-editing enzyme APOBEC-3A	Unknown	P31941
MMDBp0196668	Probable DNA dC->dU-editing enzyme APOBEC-3B	Unknown	Q9UH17
MMDBp0196669	Probable DNA dC->dU-editing enzyme APOBEC-3C	Unknown	Q9NRW3
MMDBp0196670	Probable DNA dC->dU-editing enzyme APOBEC-3D	Unknown	Q96AK3
MMDBp0196671	DNA dC->dU-editing enzyme APOBEC-3F	Unknown	Q8IUX4
MMDBp0196681	Activation-induced cytidine deaminase	Unknown	Q9GZX7

Human Pathways

Pathways

Name	SMPDB/PathBank

Microbial Pathways

Pathways

Not Available

Metabolic Reactions

Reactions

This table shows at most 20 reactions. For the full list of associated reactions:

See All Associated Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference
Argininemia		Association	Human Urine	HMDB	6796772
Canavan disease	Slight Increase	Association	Human Blood	HMDB	16139832
Degenerative disc disease		Association	Human Cerebrospinal Fluid (CSF)	HMDB	6656991
Lesch-Nyhan syndrome	Increased	Association	Human Blood	HMDB	3148065
Uremia		Association	Human Blood	HMDB	12675874

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Eukaryota	Parabasalia	1		Microbial culture
Bacteria	Firmicutes	658	Human feces; Human pleural fluid plaque; Pig ; Human ; Cattle ; Catfish	Microbial culture; Indirect association between microbiota composition and metabolites measured in host biospecimen; Metabolic reconstruction
Bacteria	Bacteroidetes	243	Human feces; Human appendix biopsy; Human	Microbial culture; Indirect association between microbiota composition and metabolites measured in host biospecimen; Metabolic reconstruction
Bacteria	Verrucomicrobia	3	Human feces; Human	Indirect association between microbiota composition and metabolites measured in host biospecimen; Metabolic reconstruction
Bacteria	Proteobacteria	478	Human feces; Human ; Human feces; pleural fluid plaque; bal; Human sputum; Human unknown; Pig ; Human pleural fluid plaque; Human dental plaque; Human nasal swab; Cattle ; River trout ; Chicken	Indirect association between microbiota composition and metabolites measured in host biospecimen; Metabolic reconstruction
Bacteria	Actinobacteria	179	Human feces; Human sputum; Human bronchial brush; Human nasopharyngeal swab; Human pleural fluid plaque; Human dental plaque; Human	Metabolic reconstruction
Bacteria	Synergistetes	5	Human feces	Metabolic reconstruction
Bacteria	Spirochaetes	14	Human feces; Human ; Relapsing fever tick	Metabolic reconstruction
Archaea	Thaumarchaeota	1	Human feces	Metabolic reconstruction
Bacteria	Fusobacteria	25	Human feces; Human	Metabolic reconstruction
Archaea	Euryarchaeota	8	Human feces; Cattle ; Human	Metabolic reconstruction
Bacteria	Candidatus Melainabacteria	2	Human feces	Metabolic reconstruction
Bacteria	Tenericutes	10	Human feces; Human	Metabolic reconstruction
Bacteria	Planctomycetes	3	Human feces	Metabolic reconstruction
Archaea	Crenarchaeota	1	Human feces	Metabolic reconstruction
Eukaryota/Fungi	Ascomycota	3	Human feces	Unknown
Bacteria/NULL	Proteobacteria	1	Human feces; Human ; Human feces; pleural fluid plaque; bal; Human sputum; Human unknown; Pig ; Human pleural fluid plaque; Human dental plaque; Human nasal swab; Cattle ; River trout ; Chicken	Indirect association between microbiota composition and metabolites measured in host biospecimen; Metabolic reconstruction
Bacteria	Chloroflexi	3
Bacteria	Chlamydiae	1	Human
Bacteria	Deinococcus-Thermus	4
Archaea/Archaea	Euryarchaeota	1	Human feces; Cattle ; Human	Metabolic reconstruction
Bacteria	Chlorobi	1

Exposure Sources

Other Exposures

Source Type	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Age	Sex	Health Condition	Data Source	Reference
Human Feces	Detected but not Quantified								HMDB
Human	Detected and Quantified	67.836		18.0896	125.497	Children (1-13 years old)	Not Specified	Arginase Deficiency	HMDB	6796772
Human	Detected and Quantified	4.23	1.92			Adult (>18 years old)	Both	Canavan disease	HMDB	16139832
Human	Detected and Quantified	2.30		1.90	2.70	Adult (>18 years old)	Both	Degenerative disc disease	HMDB	6656991
Human	Detected and Quantified	7.7	0.9			Adult (>18 years old)	Both	Lesch-Nyhan syndrome	HMDB	3148065
Human	Detected and Quantified	40.164	46.721			Adult (>18 years old)	Both	Uremia	HMDB	12675874
Human	Detected and Quantified			0	15	Newborn (0-30 days old)	Both	Normal	HMDB	31506554
Human	Detected and Quantified	0.21	0.08			Adult (>18 years old)	Both	Normal	HMDB	9129323
Human	Detected and Quantified	0.21	0.09			Adult (>18 years old)	Female	Normal	HMDB	9129323
Human	Detected and Quantified	0.22	0.07			Adult (>18 years old)	Male	Normal	HMDB	9129323
Human	Detected and Quantified	0.994		0.637	1.351	Adult (>18 years old)	Both	Normal	HMDB	15116424
Human	Detected and Quantified	1296.744		668.847	1924.641	Infant (0-1 year old)	Not Specified	Normal	HMDB	22435727
Human	Detected and Quantified	3.10		2.90	3.30	Adult (>18 years old)	Both	Normal	HMDB	6656991
Human	Detected and Quantified	3.12	1.31			Adult (>18 years old)	Both	Normal	HMDB	16139832
Human	Detected and Quantified	4.17	4.75			Adult (>18 years old)	Female	Normal	HMDB	7702711
Human	Detected and Quantified	559.647		259.349	859.946	Infant (0-1 year old)	Not Specified	Normal	HMDB	22435727
Human	Detected and Quantified	6.148	5.328			Adult (>18 years old)	Both	Normal	HMDB	12675874
Human	Detected and Quantified	7.1	3.7			Adult (>18 years old)	Female	Normal	HMDB	24027187
Human	Detected and Quantified	982.795		600.597	1364.994	Infant (0-1 year old)	Not Specified	Normal	HMDB	22435727
Human	Detected and Quantified			0	9	Children (1 - 18 years old)	Both	Normal	HMDB	BC Children's Hospital Biochemical Genetics Lab
Human	Detected and Quantified	21.1	8.4			Adult (>18 years old)	Not Specified	Normal	HMDB	Geigy Scientific Tables, 8th Rev edition, pp. 130. Edited by C. Lentner, West Cadwell, N.J.: Medical education Div., Ciba-Geigy Corp. Basel, Switzerland c1981-1992.
Human Placenta	Detected but not Quantified					Not Specified	Not Specified	Normal	HMDB	34986597
Human Feces	Detected but not Quantified					Adult (>18 years old)	Both	Normal	HMDB	21761941
Human Feces	Detected but not Quantified					Adult (>18 years old)	Both	Normal	HMDB	24029555
Human Blood	Detected but not Quantified					Adult (>18 years old)	Both	Normal	HMDB	19678709
Human Feces	Detected but not Quantified					Infant (0-1 year old)	NULL	Normal	HMDB	24628373
Human Feces	Detected but not Quantified					Infant (0-1 year old)	Not Specified	Normal	HMDB	24628373
Human Feces	Detected but not Quantified					Infant (0-1 year old)	Not Specified	Normal	HMDB	24628373
Human Feces	Detected but not Quantified					Adult (>18 years old)	Both	Normal	HMDB	27543620
Human Feces	Detected but not Quantified					Adult (>18 years old)	Both	Normal	HMDB	25037050
Human Feces	Detected but not Quantified					Adult (>18 years old)	Both	Normal	HMDB	29808030
Human Urine	Detected but not Quantified					Adult (>18 years old)	Both	Normal	HMDB	32966057
Human Blood	Detected but not Quantified					Adult (>18 years old)	Both	Normal	HMDB	32966057

External Links

HMDB ID

HMDB0000296

DrugBank ID

DB02745

Phenol Explorer Compound ID

Not Available

FooDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Wikipedia Link

METLIN ID

PubChem Compound

6029

PDB ID

Not Available

ChEBI ID

16704

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

Lee SH, Jung BH, Kim SY, Chung BC: A rapid and sensitive method for quantitation of nucleosides in human urine using liquid chromatography/mass spectrometry with direct urine injection. Rapid Commun Mass Spectrom. 2004;18(9):973-7. doi: 10.1002/rcm.1400. [PubMed:15116424 ]
Eells JT, Spector R: Purine and pyrimidine base and nucleoside concentrations in human cerebrospinal fluid and plasma. Neurochem Res. 1983 Nov;8(11):1451-7. doi: 10.1007/BF00965000. [PubMed:6656991 ]
Elshenawy S, Pinney SE, Stuart T, Doulias PT, Zura G, Parry S, Elovitz MA, Bennett MJ, Bansal A, Strauss JF 3rd, Ischiropoulos H, Simmons RA: The Metabolomic Signature of the Placenta in Spontaneous Preterm Birth. Int J Mol Sci. 2020 Feb 4;21(3). pii: ijms21031043. doi: 10.3390/ijms21031043. [PubMed:32033212 ]

Showing metabocard for Uridine (MMDBc0000094)

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