MiMeDB: Showing metabocard for Pseudouridine (MMDBc0000367)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2020-12-10 18:36:14 UTC

Update Date

2024-04-30 19:31:55 UTC

Metabolite ID

MMDBc0000367

Metabolite Identification

Common Name

Pseudouridine

Description

Pseudouridine, also known as psi-uridine or 5-ribosyluracil, belongs to the class of organic compounds known as nucleoside and nucleotide analogues. These are analogues of nucleosides and nucleotides, such as phosphonated nucleosides, C-glycosylated nucleoside bases, analogues where the sugar unit is a pyranose, and carbocyclic nucleosides. Pseudouridine specifically has its uracil attached via a carbon-carbon instead of a nitrogen-carbon glycosidic bond to the ribofuranose. It is the most prevalent of the over one hundred different modified nucleosides found in RNA (PMID: 17113994 ). Pseudouridine is a solid that is soluble in water. Pseudouridine exists in all living species, ranging from bacteria to humans, and is in all classes of RNA except mRNA. It is formed by enzymes called pseudouridine synthases, which post-transcriptionally isomerize specific uridine residues in RNA.

Structure

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

HMDB0000767
     RDKit          3D
Pseudouridine
 29 30  0  0  0  0  0  0  0  0999 V2000
    5.2921    0.8473   -0.2060 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0950    0.6308   -0.0231 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3482    0.2718   -1.0990 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0462    0.0268   -0.9396 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3716    0.1016    0.2418 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0429   -0.0569    0.3122 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.9013    0.9019    0.7525 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0909    0.4202    0.0761 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.3052    1.1916    0.3689 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1776    2.4898   -0.0682 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1211   -1.0567    0.3815 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.4275   -1.7430   -0.7857 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6846   -1.3399    0.7743 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.1971   -2.5011    0.2675 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1523    0.4727    1.3443 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5215    0.5318    2.4190 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4524    0.7170    1.1919 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.7737    0.1821   -2.0385 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5351   -0.2562   -1.8906 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3479   -0.1035   -0.8578 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8478    0.6018   -1.0201 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1659    0.7419   -0.1521 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5388    1.2723    1.4624 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2447    2.7491   -0.2739 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8428   -1.2998    1.2044 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6660   -2.6930   -0.5757 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7381   -1.3485    1.9117 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7113   -2.7174    0.6563 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0409    0.9657    2.0269 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
  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  6
  8 21  1  6
  9 22  1  0
  9 23  1  0
 10 24  1  0
 11 25  1  1
 12 26  1  0
 13 27  1  1
 14 28  1  0
 17 29  1  0
M  END


  Mrv1652309042000062D          

 17 18  0  0  1  0            999 V2000
    0.0000   -0.8436    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4311    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4311    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    0.3938    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    0.3938    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8064    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.6686    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.6674   -2.1536    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6674   -2.1536    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.4125   -2.9382    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.4125   -2.9382    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4521   -1.8986    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.8436    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8974   -3.6056    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    1.6314    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8974   -3.6056    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5619   -4.3593    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  7  1  1  1  0  0  0
  1  2  1  0  0  0  0
  2 13  2  0  0  0  0
  1  3  2  0  0  0  0
  2  4  1  0  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  4  6  1  0  0  0  0
  6 15  2  0  0  0  0
  7  8  1  0  0  0  0
  7  9  1  0  0  0  0
  8 10  1  0  0  0  0
  9 11  1  0  0  0  0
  9 12  1  6  0  0  0
 10 16  1  1  0  0  0
 10 11  1  0  0  0  0
 11 14  1  6  0  0  0
 16 17  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0000367

> <DATABASE_NAME>
MIME

> <SMILES>
OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)C1=CNC(=O)NC1=O

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

> <INCHI_KEY>
PTJWIQPHWPFNBW-GBNDHIKLSA-N

> <FORMULA>
C9H12N2O6

> <MOLECULAR_WEIGHT>
244.2014

> <EXACT_MASS>
244.069536126

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
29

> <JCHEM_AVERAGE_POLARIZABILITY>
21.794147572683546

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-2.01

> <JCHEM_LOGP>
-3.1001478630000006

> <ALOGPS_LOGS>
-0.58

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.602908039116013

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.663736427830294

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9792001006523368

> <JCHEM_POLAR_SURFACE_AREA>
128.12

> <JCHEM_REFRACTIVITY>
52.44100000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.38e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
β-pseudouridine

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0000767
     RDKit          3D
Pseudouridine
 29 30  0  0  0  0  0  0  0  0999 V2000
    5.2921    0.8473   -0.2060 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0950    0.6308   -0.0231 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3482    0.2718   -1.0990 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0462    0.0268   -0.9396 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3716    0.1016    0.2418 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0429   -0.0569    0.3122 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.9013    0.9019    0.7525 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0909    0.4202    0.0761 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.3052    1.1916    0.3689 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1776    2.4898   -0.0682 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1211   -1.0567    0.3815 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.4275   -1.7430   -0.7857 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6846   -1.3399    0.7743 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.1971   -2.5011    0.2675 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1523    0.4727    1.3443 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5215    0.5318    2.4190 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4524    0.7170    1.1919 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.7737    0.1821   -2.0385 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5351   -0.2562   -1.8906 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3479   -0.1035   -0.8578 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8478    0.6018   -1.0201 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1659    0.7419   -0.1521 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5388    1.2723    1.4624 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2447    2.7491   -0.2739 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8428   -1.2998    1.2044 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6660   -2.6930   -0.5757 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7381   -1.3485    1.9117 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7113   -2.7174    0.6563 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0409    0.9657    2.0269 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
  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  6
  8 21  1  6
  9 22  1  0
  9 23  1  0
 10 24  1  0
 11 25  1  1
 12 26  1  0
 13 27  1  1
 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  -1.575   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.334  -0.805   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.334  -0.805   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0       1.334   0.735   0.000  0.00  0.00           N+0
HETATM    5  N   UNK     0      -1.334   0.735   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0       0.000   1.505   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000  -3.115   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -1.246  -4.020   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       1.246  -4.020   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -0.770  -5.485   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.770  -5.485   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       2.711  -3.544   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       2.667  -1.575   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       1.675  -6.730   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       0.000   3.045   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      -1.675  -6.730   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0      -1.049  -8.137   0.000  0.00  0.00           O+0
CONECT    1    7    2    3                                                  
CONECT    2    1   13    4                                                  
CONECT    3    1    5                                                       
CONECT    4    2    6                                                       
CONECT    5    3    6                                                       
CONECT    6    5    4   15                                                  
CONECT    7    1    8    9                                                  
CONECT    8    7   10                                                       
CONECT    9    7   11   12                                                  
CONECT   10    8   16   11                                                  
CONECT   11    9   10   14                                                  
CONECT   12    9                                                            
CONECT   13    2                                                            
CONECT   14   11                                                            
CONECT   15    6                                                            
CONECT   16   10   17                                                       
CONECT   17   16                                                            
MASTER        0    0    0    0    0    0    0    0   17    0   36    0
END

COMPND    HMDB0000767
HETATM    1  O1  UNL     1       5.292   0.847  -0.206  1.00  0.00           O  
HETATM    2  C1  UNL     1       4.095   0.631  -0.023  1.00  0.00           C  
HETATM    3  N1  UNL     1       3.348   0.272  -1.099  1.00  0.00           N  
HETATM    4  C2  UNL     1       2.046   0.027  -0.940  1.00  0.00           C  
HETATM    5  C3  UNL     1       1.372   0.102   0.242  1.00  0.00           C  
HETATM    6  C4  UNL     1      -0.043  -0.057   0.312  1.00  0.00           C  
HETATM    7  O2  UNL     1      -0.901   0.902   0.752  1.00  0.00           O  
HETATM    8  C5  UNL     1      -2.091   0.420   0.076  1.00  0.00           C  
HETATM    9  C6  UNL     1      -3.305   1.192   0.369  1.00  0.00           C  
HETATM   10  O3  UNL     1      -3.178   2.490  -0.068  1.00  0.00           O  
HETATM   11  C7  UNL     1      -2.121  -1.057   0.382  1.00  0.00           C  
HETATM   12  O4  UNL     1      -2.428  -1.743  -0.786  1.00  0.00           O  
HETATM   13  C8  UNL     1      -0.685  -1.340   0.774  1.00  0.00           C  
HETATM   14  O5  UNL     1      -0.197  -2.501   0.267  1.00  0.00           O  
HETATM   15  C9  UNL     1       2.152   0.473   1.344  1.00  0.00           C  
HETATM   16  O6  UNL     1       1.521   0.532   2.419  1.00  0.00           O  
HETATM   17  N2  UNL     1       3.452   0.717   1.192  1.00  0.00           N  
HETATM   18  H1  UNL     1       3.774   0.182  -2.038  1.00  0.00           H  
HETATM   19  H2  UNL     1       1.535  -0.256  -1.891  1.00  0.00           H  
HETATM   20  H3  UNL     1      -0.348  -0.103  -0.858  1.00  0.00           H  
HETATM   21  H4  UNL     1      -1.848   0.602  -1.020  1.00  0.00           H  
HETATM   22  H5  UNL     1      -4.166   0.742  -0.152  1.00  0.00           H  
HETATM   23  H6  UNL     1      -3.539   1.272   1.462  1.00  0.00           H  
HETATM   24  H7  UNL     1      -2.245   2.749  -0.274  1.00  0.00           H  
HETATM   25  H8  UNL     1      -2.843  -1.300   1.204  1.00  0.00           H  
HETATM   26  H9  UNL     1      -2.666  -2.693  -0.576  1.00  0.00           H  
HETATM   27  H10 UNL     1      -0.738  -1.348   1.912  1.00  0.00           H  
HETATM   28  H11 UNL     1       0.711  -2.717   0.656  1.00  0.00           H  
HETATM   29  H12 UNL     1       4.041   0.966   2.027  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3   17
CONECT    3    4   18
CONECT    4    5    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

HMDB0000767
     RDKit          3D
Pseudouridine
 29 30  0  0  0  0  0  0  0  0999 V2000
    5.2921    0.8473   -0.2060 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0950    0.6308   -0.0231 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3482    0.2718   -1.0990 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0462    0.0268   -0.9396 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3716    0.1016    0.2418 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0429   -0.0569    0.3122 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.9013    0.9019    0.7525 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0909    0.4202    0.0761 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.3052    1.1916    0.3689 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1776    2.4898   -0.0682 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1211   -1.0567    0.3815 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.4275   -1.7430   -0.7857 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6846   -1.3399    0.7743 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.1971   -2.5011    0.2675 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1523    0.4727    1.3443 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5215    0.5318    2.4190 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4524    0.7170    1.1919 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.7737    0.1821   -2.0385 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5351   -0.2562   -1.8906 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3479   -0.1035   -0.8578 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8478    0.6018   -1.0201 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1659    0.7419   -0.1521 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5388    1.2723    1.4624 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2447    2.7491   -0.2739 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8428   -1.2998    1.2044 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6660   -2.6930   -0.5757 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7381   -1.3485    1.9117 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7113   -2.7174    0.6563 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0409    0.9657    2.0269 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
  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  6
  8 21  1  6
  9 22  1  0
  9 23  1  0
 10 24  1  0
 11 25  1  1
 12 26  1  0
 13 27  1  1
 14 28  1  0
 17 29  1  0
M  END

Synonyms

Value	Source
(1S)-1,4-Anhydro-1-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-D-ribitol	ChEBI
5-(beta-D-Ribofuranosyl)uracil	ChEBI
beta-Pseudouridine	ChEBI
p	ChEBI
Psi-uridine	ChEBI
5-(b-D-Ribofuranosyl)uracil	Generator
5-(Β-D-ribofuranosyl)uracil	Generator
b-Pseudouridine	Generator
Β-pseudouridine	Generator
5-(b-delta-Ribofuranosyl)uracil	HMDB
5-b-D-Ribofuranosyl-uracil	HMDB
5-beta-delta-Ribofuranosyl-uracil	HMDB
5-Ribosyluracil	HMDB
b-D-Pseudouridine	HMDB
beta-delta-Pseudouridine	HMDB
Pseudouridine C	HMDB
Y-uridine	HMDB
5-beta-D-Ribofuranosyl-2,4(1H,3H)-pyrimidinedione	HMDB
5-Β-D-ribofuranosyl-2,4(1H,3H)-pyrimidinedione	HMDB
beta-D-Pseudouridine	HMDB
Β-D-pseudouridine	HMDB
Ψ-uridine	HMDB
Pseudouridine	HMDB

Molecular Formula

C₉H₁₂N₂O₆

Average Mass

244.2014

Monoisotopic Mass

244.069536126

IUPAC Name

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

Traditional Name

β-pseudouridine

CAS Registry Number

Not Available

SMILES

OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)C1=CNC(=O)NC1=O

InChI Identifier

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

InChI Key

PTJWIQPHWPFNBW-GBNDHIKLSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as nucleoside and nucleotide analogues. These are analogues of nucleosides and nucleotides. These include phosphonated nucleosides, C-glycosylated nucleoside bases, analogues where the sugar unit is a pyranose, and carbocyclic nucleosides, among others.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Nucleoside and nucleotide analogues

Sub Class

Not Available

Direct Parent

Nucleoside and nucleotide analogues

Alternative Parents

Substituents

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

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

pseudouridines (CHEBI:17802 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	63.8 g/L	ALOGPS
logP	-2	ALOGPS
logP	-3.1	ChemAxon
logS	-0.58	ALOGPS
pKa (Strongest Acidic)	8.66	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	128.12 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	52.44 m³·mol⁻¹	ChemAxon
Polarizability	21.79 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

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0unc-7930000000-a1e7f343c88a63ac1976	2016-09-22	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positive	splash10-0fi0-3494100000-8d726ed412554c1f92f0	2017-10-06	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_4) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_5) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_1) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_2) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_3) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_4) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_5) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_6) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_7) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_8) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_9) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_10) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_2) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_3) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_4) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_5) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_6) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_7) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-IT , negative	splash10-0udi-0900000000-6ade42aaa885371e176c	2017-09-14	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF 10V, positive	splash10-0a4i-0190000000-129f123affa0ecbf7a59	2020-07-21	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF 20V, positive	splash10-052f-0910000000-302fbdef606070bd5a67	2020-07-21	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF 40V, positive	splash10-001i-9300000000-11f5761be16d1b061df5	2020-07-21	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 30V, Negative	splash10-0006-9600000000-7585746143c62ab3f832	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 40V, Negative	splash10-0006-9100000000-010da2c57a936868eecc	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 40V, Positive	splash10-0kai-9200000000-12f986238bdf05dc39b9	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 30V, Positive	splash10-001i-9400000000-b6dbdfa2d4643fc13e70	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 10V, Positive	splash10-0a4i-0190000000-129f123affa0ecbf7a59	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 20V, Positive	splash10-052f-0910000000-302fbdef606070bd5a67	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 0V, Positive	splash10-0bta-0890000000-2b3810ae2bbe68268b17	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 40V, Positive	splash10-001i-9300000000-7e64dc8404ac65411358	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 0V, Positive	splash10-052b-0290000000-7cf7d5be6f7a84299cab	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 10V, Positive	splash10-0a4i-0950000000-de2a45f204636756b9c4	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 30V, Positive	splash10-00l6-9000000000-b4060d47530bdf70d6cc	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 10V, Positive	splash10-0a4i-3920000000-15bb158a77906d0f87b5	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 20V, Negative	splash10-0udi-2900000000-600643d24abd3ba9b5f1	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 10V, Negative	splash10-0udi-0920000000-a73049fd7001db7f72d5	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 20V, Negative	splash10-0udi-0900000000-46e1b064445ad43a60fd	2021-09-20	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0002-0490000000-226d044c24dd80a7c2ca	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0h0s-2980000000-add34ee37b95c102114d	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-06rm-5900000000-8d66d80928e84e9c93fd	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0006-9360000000-3bd8fcdd66c5d245778e	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0006-9210000000-f551740a13c90ff1d324	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0006-9000000000-bf4e4234a47d8aa03828	2015-09-15	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, experimental)		2012-12-04	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-29	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm

Biospecimen Locations

Amniotic Fluid
Blood
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
MMDBp0192704	tRNA pseudouridine synthase A, mitochondrial	Enzyme	Q9Y606	Homo sapiens
MMDBp0193196	H/ACA ribonucleoprotein complex subunit 4	Enzyme	O60832	Homo sapiens
MMDBp0195902	Putative tRNA pseudouridine synthase Pus10	Enzyme	Q3MIT2	Homo sapiens
MMDBp0195903	tRNA pseudouridine synthase 3	Enzyme	Q9BZE2	Homo sapiens
MMDBp0195904	Pseudouridylate synthase 7 homolog	Enzyme	Q96PZ0	Homo sapiens
MMDBp0195905	Pseudouridylate synthase 7 homolog-like protein	Enzyme	Q9H0K6	Homo sapiens
MMDBp0195906	RNA pseudouridylate synthase domain-containing protein 1	Enzyme	Q9UJJ7	Homo sapiens
MMDBp0195907	RNA pseudouridylate synthase domain-containing protein 2	Enzyme	Q8IZ73	Homo sapiens
MMDBp0195908	RNA pseudouridylate synthase domain-containing protein 3	Enzyme	Q6P087	Homo sapiens
MMDBp0195909	RNA pseudouridylate synthase domain-containing protein 4	Enzyme	Q96CM3	Homo sapiens
MMDBp0195910	Probable tRNA pseudouridine synthase 1	Enzyme	Q8WWH5	Homo sapiens
MMDBp0195911	Probable tRNA pseudouridine synthase 2	Enzyme	O95900	Homo sapiens
MMDBp0196233	tRNA pseudouridine synthase-like 1	Enzyme	Q8N0Z8	Homo sapiens
MMDBp0196835	Pseudouridine-5'-monophosphatase	Unknown	Q08623

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0014211	Adenosine triphosphate	ADP	Pseudouridine kinase	Phosphorylation	RHEA	34755880
MMDBr0018836	Pseudouridine	Hydrogen Ion	Pseudouridine kinase	Phosphorylation	PathBank	31602464

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference
Canavan disease	Increased	Association	Human Blood	HMDB	16139832
Uremia		Association	Human Blood	HMDB	12675874

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria	Bacteroidetes	3	Human feces; Human stool; Human	Indirect association between microbiota composition and metabolites measured in host biospecimen
Bacteria	Firmicutes	9	Human stool; Human ; Human feces; Human urine; Human mucosa; Human supragingival plaque; Human saliva; Human subgingival plaque	Indirect association between microbiota composition and metabolites measured in host biospecimen
Bacteria	Proteobacteria	3	Human feces; Human stool; Human ; Human mucosa; Human supragingival plaque; Human saliva; Human subgingival plaque	Indirect association between microbiota composition and metabolites measured in host biospecimen
Eukaryota/Fungi	Ascomycota	2	Human feces; Human saliva	Unknown

Exposure Sources

Source Type	Source Sub-type	Species	Data Source	Reference
Animal		Haliotis	FooDB	31437929
Animal		Strombidae	FooDB	31437929
Animal		Clupea harengus harengus	FooDB	31437929
Animal	Milk	Bos taurus	FooDB	31437929
Animal		Undaria pinnatifida	FooDB	31437929
Animal		Peprilus triacanthus	FooDB	31437929
Animal		Rhodophyta	FooDB	31437929
Animal		Myoxocephalus	FooDB	31437929
Animal		Eucheuma	FooDB	31437929
Animal		Saccharina japonica	FooDB	31437929
Animal		Spirulina	FooDB	31437929
Animal		Lota lota	FooDB	31437929
Animal		Porphyra umbilicalis	FooDB	31437929
Animal		Chondrus crispus	FooDB	31437929
Animal		Laminaria	FooDB	31437929
Plant		Diospyros virginiana	FooDB	31437929
Plant		Origanum x majoricum	FooDB	31437929
Plant		Lactuca sativa l. var. longifolia	FooDB	31437929
Plant		Rumex	FooDB	31437929
Plant		Rubus x loganobaccus	FooDB	31437929
Plant		Tragopogon porrifolius	FooDB	31437929
Plant		Allium ascalonicum	FooDB	31437929
Plant		Citrullus lanatus var. fistulosus	FooDB	31437929
Plant		Rubus chamaemorus	FooDB	31437929
Plant		Amelanchier alnifolia	FooDB	31437929
Plant		Eugenia uniflora	FooDB	31437929
Plant		Taraxacum officinale	FooDB	31437929
Plant		Annona reticulata	FooDB	31437929
Plant		Curcuma longa	FooDB	31437929
Plant		Sesbania bispinosa	FooDB	31437929
Plant		Elettaria cardamomum	FooDB	31437929
Plant		Ribes x nidigrolaria	FooDB	31437929
Plant		Ananas comosus	FooDB	31437929
Plant		Persea americana	FooDB	31437929
Plant		Garcinia mangostana	FooDB	31437929
Plant		Dioscorea pentaphylla	FooDB	31437929
Plant		Allium tuberosum	FooDB	31437929
Plant		Lathyrus sativus	FooDB	31437929
Plant		Brassica oleracea var. botrytis	FooDB	31437929
Plant		Cichorium intybus	FooDB	31437929
Plant		Corchorus olitorius	FooDB	31437929
Plant		Chenopodium quinoa	FooDB	31437929
Plant		Cucumis melo	FooDB	31437929
Plant		Juglans nigra	FooDB	31437929
Plant		Gaylussacia baccata	FooDB	31437929
Plant		Petasites japonicus	FooDB	31437929
Plant		Prunus tomentosa	FooDB	31437929
Plant		Maranta arundinacea	FooDB	31437929
Plant		Mentha x piperita	FooDB	31437929
Plant		Cinnamomum verum	FooDB	31437929
Plant		Matteuccia struthiopteris	FooDB	31437929
Plant		Cucurbita moschata	FooDB	31437929
Plant		Vaccinium myrtilloides	FooDB	31437929
Plant		Tilia	FooDB	31437929
Plant		Macadamia	FooDB	31437929
Plant		Ocimum basilicum	FooDB	31437929
Plant		Nelumbo	FooDB	31437929
Plant		Rosa	FooDB	31437929
Plant		Apium graveolens var. rapaceum	FooDB	31437929
Plant		Papaver	FooDB	31437929
Plant		Brassica oleracea var. conica	FooDB	31437929
Plant		Glycine max	FooDB	31437929
Plant		Capsicum annuum var. annuum	FooDB	31437929
Plant		Citrus limon	FooDB	31437929
Plant		Lippia graveolens	FooDB	31437929
Plant		Annona cherimola	FooDB	31437929
Plant		Brassica rapa var. pekinensis	FooDB	31437929
Plant		Brassica rapa	FooDB	31437929
Plant		Sesamum orientale	FooDB	31437929
Plant		Prunus	FooDB	31437929
Plant		Capparis spinosa	FooDB	31437929
Plant		Vaccinium deliciosum	FooDB	31437929
Plant		Citrus sinensis	FooDB	31437929
Plant		Artocarpus heterophyllus	FooDB	31437929
Plant		Prunus virginiana	FooDB	31437929
Plant		Lens culinaris	FooDB	31437929
Plant		Phaseolus lunatus	FooDB	31437929
Plant		Macadamia tetraphylla	FooDB	31437929
Plant		Musa acuminata	FooDB	31437929
Plant		Carissa macrocarpa	FooDB	31437929
Plant		Citrullus lanatus	FooDB	31437929
Plant		Lagenaria siceraria	FooDB	31437929
Plant		Linum usitatissimum	FooDB	31437929
Plant		Vigna unguiculata ssp. unguiculata	FooDB	31437929
Plant		Satureja hortensis	FooDB	31437929
Plant		Sorbus aucuparia	FooDB	31437929
Plant		Phyllostachys edulis	FooDB	31437929
Plant		Averrhoa carambola	FooDB	31437929
Plant		Carum carvi	FooDB	31437929
Plant		Allium schoenoprasum	FooDB	31437929
Plant		Citrus reticulata	FooDB	31437929
Plant		Prunus domestica	FooDB	31437929
Plant		Prunus armeniaca	FooDB	31437929
Plant		Brassica oleracea var. costata	FooDB	31437929
Plant		Panax	FooDB	31437929
Plant		Nelumbo nucifera	FooDB	31437929
Plant		Brassica rapa var. rapa	FooDB	31437929
Plant		Cymbopogon citratus	FooDB	31437929
Plant		Bertholletia excelsa	FooDB	31437929
Plant		Ceratonia siliqua	FooDB	31437929
Plant		Vigna umbellata	FooDB	31437929
Plant		Luffa aegyptiaca	FooDB	31437929
Plant		Anethum graveolens	FooDB	31437929
Plant		Coriandrum sativum	FooDB	31437929
Plant		Rubus occidentalis	FooDB	31437929
Plant		Allium fistulosum	FooDB	31437929
Plant		Capsicum	FooDB	31437929
Plant		Tilia cordata	FooDB	31437929
Plant		Carthamus tinctorius	FooDB	31437929
Plant		Lupinus	FooDB	31437929
Plant		Vaccinium alaskaense	FooDB	31437929
Plant		Cicer arietinum	FooDB	31437929
Plant		Durio zibethinus	FooDB	31437929
Plant		Anacardium occidentale	FooDB	31437929
Plant		Prunus persica var. nucipersica	FooDB	31437929
Plant		Eriobotrya japonica	FooDB	31437929
Plant		Ribes glandulosum	FooDB	31437929
Plant		Brassica napus var. pabularia	FooDB	31437929
Plant		Verbena officinalis	FooDB	31437929
Plant		Oenothera biennis	FooDB	31437929
Plant		Vaccinium oxycoccos	FooDB	31437929
Plant		Diospyros kaki	FooDB	31437929
Plant		Rumex acetosa	FooDB	31437929
Plant		Virola surinamensis	FooDB	31437929
Plant		Theobroma cacao	FooDB	31437929
Plant		Camellia sinensis	FooDB	31437929
Plant		Aloysia triphylla	FooDB	31437929
Plant		Vaccinium parvifolium	FooDB	31437929
Plant		Solanum lycopersicum var. lycopersicum	FooDB	31437929
Plant		Capsicum chinense	FooDB	31437929
Plant		Brassica oleracea var. capitata	FooDB	31437929
Plant		Pyrus pyrifolia	FooDB	31437929
Plant		Vaccinium reticulatum	FooDB	31437929
Plant		Solanum quitoense	FooDB	31437929
Plant		Vaccinium myrtillus	FooDB	31437929
Plant		Phaseolus vulgaris	FooDB	31437929
Plant		Daucus carota ssp. sativus	FooDB	31437929
Plant		Theobroma grandiflorum	FooDB	31437929
Plant		Syzygium aromaticum	FooDB	31437929
Plant		Vigna unguiculata ssp. cylindrica	FooDB	31437929
Plant		Ginkgo biloba	FooDB	31437929
Plant		Satureja montana	FooDB	31437929
Plant		Perideridia oregana	FooDB	31437929
Plant			FooDB	31437929
Plant		Flammulina velutipes	FooDB	31437929
Plant		Vaccinium arboreum	FooDB	31437929
Plant		Citrus japonica	FooDB	31437929
Plant		Wasabia japonica	FooDB	31437929
Plant		Origanum onites	FooDB	31437929
Plant		Vicia faba	FooDB	31437929
Plant		Pouteria sapota	FooDB	31437929
Plant		Prunus avium	FooDB	31437929
Plant		Viburnum edule	FooDB	31437929
Plant		Piper nigrum	FooDB	31437929
Plant		Vitis vinifera	FooDB	31437929
Plant		Vaccinium uliginosum	FooDB	31437929
Plant		Dioscorea	FooDB	31437929
Plant		Origanum vulgare	FooDB	31437929
Plant		Capsicum annuum	FooDB	31437929
Plant		Momordica charantia	FooDB	31437929
Plant		Castanea	FooDB	31437929
Plant		Rubus ursinus x idaeus	FooDB	31437929
Plant		Cirsium	FooDB	31437929
Plant		Raphanus sativus var. sativus	FooDB	31437929
Plant		Opuntia	FooDB	31437929
Plant		Prunus persica var. persica	FooDB	31437929
Plant		Pleurotus ostreatus	FooDB	31437929
Plant		Colocasia esculenta	FooDB	31437929
Plant		Brassica oleracea var. italica	FooDB	31437929
Plant		Anthriscus cerefolium	FooDB	31437929
Plant		Solanum melongena	FooDB	31437929
Plant		Nuphar lutea	FooDB	31437929
Plant		Pachyrhizus erosus	FooDB	31437929
Plant		Lupinus albus	FooDB	31437929
Plant		Dysphania ambrosioides	FooDB	31437929
Plant		Cichorium endivia	FooDB	31437929
Plant		Raphanus sativus var. niger	FooDB	31437929
Plant		Myristica fragrans	FooDB	31437929
Plant		Elaeis	FooDB	31437929
Plant		Cinnamomum	FooDB	31437929
Plant		Photinia melanocarpa	FooDB	31437929
Plant		Ribes uva-crispa	FooDB	31437929
Plant		Feijoa sellowiana	FooDB	31437929
Plant		Vaccinium	FooDB	31437929
Plant		Apium graveolens	FooDB	31437929
Plant		Syzygium jambos	FooDB	31437929
Plant		Rheum rhabarbarum	FooDB	31437929
Plant		Crocus sativus	FooDB	31437929
Plant		Salix pulchra	FooDB	31437929
Plant		Lablab purpureus	FooDB	31437929
Plant		Fagus	FooDB	31437929
Plant		Citrus maxima	FooDB	31437929
Plant		Cydonia oblonga	FooDB	31437929
Plant		Castanea sativa	FooDB	31437929
Plant		Salvia officinalis	FooDB	31437929
Plant		Vaccinium ovatum	FooDB	31437929
Plant		Opuntia cochenillifera	FooDB	31437929
Plant		Annona muricata	FooDB	31437929
Plant		Thymus pulegioides	FooDB	31437929
Plant		Mespilus germanica	FooDB	31437929
Plant		Cucurbita	FooDB	31437929
Plant		Phaseolus coccineus	FooDB	31437929
Plant		Brassica rapa var. perviridis	FooDB	31437929
Plant		Cocos nucifera	FooDB	31437929
Plant		Tamarindus indica	FooDB	31437929
Plant		Mentha aquatica	FooDB	31437929
Plant		Salvia elegans	FooDB	31437929
Plant		Mentha	FooDB	31437929
Plant		Cucurbita pepo var. cylindrica	FooDB	31437929
Plant		Sagittaria latifolia	FooDB	31437929
Plant		Sambucus	FooDB	31437929
Plant		Syzygium cumini	FooDB	31437929
Plant		Typha angustifolia	FooDB	31437929
Plant		Psidium guajava	FooDB	31437929
Plant		Empetrum nigrum	FooDB	31437929
Plant		Myrica rubra	FooDB	31437929
Plant		Pinus	FooDB	31437929
Plant		Tilia tomentosa	FooDB	31437929
Plant		Olea europaea	FooDB	31437929
Plant		Valerianella locusta	FooDB	31437929
Plant		Vaccinium angustifolium x vaccinium corymbosum	FooDB	31437929
Plant		Sisymbrium	FooDB	31437929
Plant		Daucus carota	FooDB	31437929
Plant		Vaccinium vitis-idaea	FooDB	31437929
Plant		Solanum tuberosum	FooDB	31437929
Plant		Vanilla	FooDB	31437929
Plant		Carya	FooDB	31437929
Plant		Borago officinalis	FooDB	31437929
Plant		Physalis philadelphica var. immaculata	FooDB	31437929
Plant		Scorzonera hispanica	FooDB	31437929
Plant		Vigna unguiculata ssp. sesquipedalis	FooDB	31437929
Plant		Hyssopus officinalis	FooDB	31437929
Plant		Manihot esculenta	FooDB	31437929
Plant		Angelica keiskei	FooDB	31437929
Plant		Raphanus sativus	FooDB	31437929
Plant		Brassica oleracea l. var. capitata l. f. alba dc.	FooDB	31437929
Plant		Ipomoea aquatica	FooDB	31437929
Plant		Beta vulgaris ssp. cicla	FooDB	31437929
Plant		Prunus dulcis	FooDB	31437929
Plant		Rubus spectabilis	FooDB	31437929
Plant		Vigna radiata	FooDB	31437929
Plant		Musa x paradisiaca	FooDB	31437929
Plant		Allium sativum	FooDB	31437929
Plant		Cantharellus cibarius	FooDB	31437929
Plant		Cuminum cyminum	FooDB	31437929
Plant		Sinapis alba	FooDB	31437929
Plant		Brassica ruvo	FooDB	31437929
Plant		Fragaria x ananassa	FooDB	31437929
Plant		Pyrus communis	FooDB	31437929
Plant		Morus nigra	FooDB	31437929
Plant		Apium graveolens var. secalinum	FooDB	31437929
Plant		Rubus idaeus	FooDB	31437929
Plant		Arachis hypogaea	FooDB	31437929
Plant		Pinus edulis	FooDB	31437929
Plant		Abelmoschus esculentus	FooDB	31437929
Plant		Opuntia macrorhiza	FooDB	31437929
Plant		Solanum lycopersicum	FooDB	31437929
Plant		Moringa oleifera	FooDB	31437929
Plant		Passiflora edulis	FooDB	31437929
Plant		Manilkara zapota	FooDB	31437929
Plant		Vigna angularis	FooDB	31437929
Plant		Allium cepa	FooDB	31437929
Plant		Malus	FooDB	31437929
Plant		Mentha spicata	FooDB	31437929
Plant		Cucurbita pepo var. clypeata	FooDB	31437929
Plant		Corylus	FooDB	31437929
Plant		Juglans	FooDB	31437929
Plant		Sambucus nigra	FooDB	31437929
Plant			FooDB	31437929
Plant		Mangifera indica	FooDB	31437929
Plant		Illicium verum	FooDB	31437929
Plant		Helianthus annuus	FooDB	31437929
Plant		Ribes nigrum	FooDB	31437929
Plant		Chamaemelum nobile	FooDB	31437929
Plant		Auricularia auricula-judae	FooDB	31437929
Plant		Zingiber officinale	FooDB	31437929
Plant		Laurus nobilis	FooDB	31437929
Plant		Petroselinum crispum	FooDB	31437929
Plant		Juglans ailanthifolia	FooDB	31437929
Plant		Attalea speciosa	FooDB	31437929
Plant		Pisum sativum	FooDB	31437929
Plant		Polygonum alpinum	FooDB	31437929
Plant		Hippophae rhamnoides	FooDB	31437929
Plant		Melissa officinalis	FooDB	31437929
Plant		Pediomelum esculentum	FooDB	31437929
Plant		Auricularia polytricha	FooDB	31437929
Plant		Brassica juncea	FooDB	31437929
Plant		Vaccinium corymbosum	FooDB	31437929
Plant		Camellia oleifera	FooDB	31437929
Plant		Chrysanthemum coronarium	FooDB	31437929
Plant		Eleocharis dulcis	FooDB	31437929
Plant		Actinidia chinensis	FooDB	31437929
Plant		Rubus arcticus	FooDB	31437929
Plant		Spinacia oleracea	FooDB	31437929
Plant		Carica papaya	FooDB	31437929
Plant		Thymus vulgaris	FooDB	31437929
Plant		Pimenta dioica	FooDB	31437929
Plant		Rumex articus	FooDB	31437929
Plant		Medicago sativa	FooDB	31437929
Plant		Hibiscus sabdariffa	FooDB	31437929
Plant		Agaricus bisporus	FooDB	31437929
Plant		Vigna mungo	FooDB	31437929
Plant		Canarium ovatum	FooDB	31437929
Plant		Ribes aureum var. villosum	FooDB	31437929
Plant		Benincasa hispida	FooDB	31437929
Plant		Cajanus cajan	FooDB	31437929
Plant		Armoracia rusticana	FooDB	31437929
Plant		Origanum majorana	FooDB	31437929
Plant		Cucurbita pepo var. cylindrica	FooDB	31437929
Plant		Prunus persica	FooDB	31437929
Plant		Eruca vesicaria ssp. sativa	FooDB	31437929
Plant		Juglans cinerea	FooDB	31437929
Plant		Vaccinium macrocarpon	FooDB	31437929
Plant		Brassica oleracea var. gongylodes	FooDB	31437929
Plant		Brassica oleracea var. gemmifera	FooDB	31437929
Plant		Foeniculum vulgare	FooDB	31437929
Plant		Arctium lappa	FooDB	31437929
Plant		Phoenix dactylifera	FooDB	31437929
Plant		Metroxylon sagu	FooDB	31437929
Plant		Artocarpus altilis	FooDB	31437929
Plant		Vitis rotundifolia	FooDB	31437929
Plant		Psidium cattleianum	FooDB	31437929
Plant		Cyathea	FooDB	31437929
Plant		Vigna unguiculata	FooDB	31437929
Plant		Brosimum alicastrum	FooDB	31437929
Plant		Cynara scolymus	FooDB	31437929
Plant		Castanea mollissima	FooDB	31437929
Plant			FooDB	31437929
Plant		Prunus cerasus	FooDB	31437929
Plant		Rosmarinus officinalis	FooDB	31437929
Plant		Lentinus edodes	FooDB	31437929
Plant		Citrus x paradisi	FooDB	31437929
Plant		Morus	FooDB	31437929
Plant		Ficus carica	FooDB	31437929
Plant		Vitis labrusca	FooDB	31437929
Plant		Lepidium sativum	FooDB	31437929
Plant		Phytolacca americana	FooDB	31437929
Plant		Beta vulgaris var. rubra	FooDB	31437929
Plant		Helianthus tuberosus	FooDB	31437929
Plant		Cucumis metuliferus	FooDB	31437929
Plant		Myrica	FooDB	31437929
Plant		Grifola frondosa	FooDB	31437929
Plant		Nephelium lappaceum	FooDB	31437929
Plant		Tetragonia tetragonioides	FooDB	31437929
Plant		Artemisia vulgaris	FooDB	31437929
Plant		Castanea crenata	FooDB	31437929
Plant		Quercus	FooDB	31437929
Plant		Corylus avellana	FooDB	31437929
Plant		Vaccinium angustifolium	FooDB	31437929
Plant		Litchi chinensis	FooDB	31437929
Plant		Physalis	FooDB	31437929
Plant		Malpighia emarginata	FooDB	31437929
Plant		Thelesperma	FooDB	31437929
Plant		Juglans regia	FooDB	31437929
Plant		Trigonella foenum-graecum	FooDB	31437929
Plant		Chamerion angustifolium	FooDB	31437929
Plant		Brassica oleracea var. sabauda	FooDB	31437929
Plant			FooDB	31437929
Plant		Vaccinium elliottii	FooDB	31437929
Plant		Brassica napus	FooDB	31437929
Plant		Levisticum officinale	FooDB	31437929
Plant		Asparagus officinalis	FooDB	31437929
Plant		Ziziphus zizyphus	FooDB	31437929
Plant		Dimocarpus longan	FooDB	31437929
Plant		Salvia hispanica	FooDB	31437929
Plant		Citrus aurantiifolia	FooDB	31437929
Plant		Cynara cardunculus	FooDB	31437929
Plant		Pangium edule	FooDB	31437929
Plant		Matricaria recutita	FooDB	31437929
Plant		Lactuca sativa	FooDB	31437929
Plant		Pimpinella anisum	FooDB	31437929
Plant		Vitellaria paradoxa	FooDB	31437929
Plant		Allium	FooDB	31437929
Plant		Artemisia dracunculus	FooDB	31437929
Plant		Brassica oleracea var. viridis	FooDB	31437929
Plant		Agave	FooDB	31437929
Plant		Hedysarum alpinum	FooDB	31437929
Plant		Eragrostis tef	FooDB	31437929
Plant		Vigna aconitifolia	FooDB	31437929
Plant		Pistacia vera	FooDB	31437929
Plant		Diospyros	FooDB	31437929
Plant		Amaranthus	FooDB	31437929
Plant		Mammea americana	FooDB	31437929
Plant		Malus pumila	FooDB	31437929
Plant		Punica granatum	FooDB	31437929
Plant		Annona squamosa	FooDB	31437929
Plant		Gossypium	FooDB	31437929
Plant		Brassica alboglabra	FooDB	31437929
Plant		Apium graveolens var. dulce	FooDB	31437929
Plant		Beta vulgaris	FooDB	31437929
Plant		Xanthosoma sagittifolium	FooDB	31437929
Plant		Basella alba	FooDB	31437929
Plant		Capsicum baccatum var. baccatum	FooDB	31437929
Plant		Vitis	FooDB	31437929
Plant		Citrus latifolia	FooDB	31437929
Plant		Byrsonima crassifolia	FooDB	31437929
Plant		Capsicum pubescens	FooDB	31437929
Plant			FooDB	31437929
Plant		Carya illinoinensis	FooDB	31437929
Plant		Crateva religiosa	FooDB	31437929
Plant		Vitis aestivalis	FooDB	31437929
Plant		Eugenia javanica	FooDB	31437929
Plant		Mentha arvensis	FooDB	31437929
Plant		Cucumis sativus	FooDB	31437929
Plant		Vaccinium stamineum	FooDB	31437929
Plant			FooDB	31437929
Plant		Brassica rapa var. chinensis	FooDB	31437929
Plant		Cinnamomum aromaticum	FooDB	31437929
Plant		Psophocarpus tetragonolobus	FooDB	31437929
Plant		Ribes rubrum	FooDB	31437929
Plant		Portulaca oleracea	FooDB	31437929
Plant		Ipomoea batatas	FooDB	31437929
Plant		Solanum lycopersicum var. cerasiforme	FooDB	31437929
Plant		Allium ampeloprasum	FooDB	31437929
Plant		Chenopodium album	FooDB	31437929
Plant		Grataegosorbus mitschurinii	FooDB	31437929
Plant		Pastinaca sativa	FooDB	31437929
Plant		Cucurbita maxima	FooDB	31437929
Plant		Sechium edule	FooDB	31437929
Plant		Brassica oleracea	FooDB	31437929

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference
Human Blood	Detected and Quantified	16.70	3.72			uM	Adult (>18 years old)	Both	Canavan disease	HMDB	16139832
Human Blood	Detected and Quantified	53.689	87.705			uM	Children (3 months - 6 years old)	Not Specified	Uremia	HMDB	12675874
Human Amniotic fluid	Detected and Quantified	1.29	1.07			uM	Adult (>18 years old)	Female	Normal	HMDB	16139832
Human Urine	Detected and Quantified	13.467		8.307	18.627	umol/mmol creatinine	Adult (>18 years old)	Both	Normal	HMDB	15116424
Human Blood	Detected and Quantified	2.0492	23.770			uM	Children (3 months - 6 years old)	Not Specified	Normal	HMDB	12675874
Human Urine	Detected and Quantified	25.0	5.0			umol/mmol creatinine	Adult (>18 years old)	Male	Normal	HMDB	9129323
Human Urine	Detected and Quantified	25.5	4.8			umol/mmol creatinine	Adult (>18 years old)	Both	Normal	HMDB	9129323
Human Urine	Detected and Quantified	26.02	4.62			umol/mmol creatinine	Adult (>18 years old)	Female	Normal	HMDB	9129323
Human Urine	Detected and Quantified	28.9		13.3	41.3	umol/mmol creatinine	Adult (>18 years old)	Both	Normal	HMDB	24023812
Human Urine	Detected and Quantified	29.8		21.8	47.3	umol/mmol creatinine	Adult (>18 years old)	Both	Normal	HMDB	24023812
Human Blood	Detected and Quantified	3.18	0.99			uM	Adult (>18 years old)	Both	Normal	HMDB	16139832
Human Urine	Detected and Quantified	63.47	32.76			umol/mmol creatinine	Infant (0-1 year old)	Both	Normal	HMDB	2026685
Human Urine	Detected and Quantified	12.5		6.5	20.4	umol/mmol creatinine	Adult (>18 years old)	Both	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 Urine	Detected but not Quantified						Adult (>18 years old)	Both	Normal	HMDB	24023812
Human Urine	Detected but not Quantified						Adult (>18 years old)	Both	Normal	HMDB	21389975
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

External Links

HMDB ID

HMDB0000767

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Not Available

Wikipedia Link

Pseudouridine

METLIN ID

5734

PubChem Compound

15047

PDB ID

Not Available

ChEBI ID

17802

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Uziel M, Smith LH, Taylor SA: Modified nucleosides in urine: selective removal and analysis. Clin Chem. 1976 Sep;22(9):1451-5. [PubMed:954194 ]
Shoemaker JD, Elliott WH: Automated screening of urine samples for carbohydrates, organic and amino acids after treatment with urease. J Chromatogr. 1991 Jan 2;562(1-2):125-38. doi: 10.1016/0378-4347(91)80571-s. [PubMed:2026685 ]
Bernert JT Jr, Bell CJ, Guntupalli J, Hannon WH: Pseudouridine is unsuitable as an endogenous renal clearance marker. Clin Chem. 1988 Jun;34(6):1011-7. [PubMed:3378317 ]
Colonna A, Russo T, Esposito F, Salvatore F, Cimino F: Determination of pseudouridine and other nucleosides in human blood serum by high-performance liquid chromatography. Anal Biochem. 1983 Apr 1;130(1):19-26. doi: 10.1016/0003-2697(83)90644-9. [PubMed:6869800 ]
Woodcock TM, Chou TC, Tan CT, Sternberg SS, Philips FS, Young CW, Burchenal JH: Biochemical, pharmacological, and phase I clinical evaluation of pseudoisocytidine. Cancer Res. 1980 Nov;40(11):4243-9. [PubMed:7471064 ]
Mak TW, Ho SS, Ho CS, Jones MG, Lai CK, Lam CW: Pleural fluid pseudouridine in malignant and benign pleural effusions. Ann Clin Biochem. 1998 Jan;35 ( Pt 1):94-8. doi: 10.1177/000456329803500112. [PubMed:9463745 ]
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Showing metabocard for Pseudouridine (MMDBc0000367)

MOL for #<Metabolite:0x00007fa4e030a200>

3D MOL for #<Metabolite:0x00007fa4e030a200>

3D SDF for #<Metabolite:0x00007fa4e030a200>

3D-SDF for #<Metabolite:0x00007fa4e030a200>

PDB for #<Metabolite:0x00007fa4e030a200>

3D PDB for #<Metabolite:0x00007fa4e030a200>

SMILES for #<Metabolite:0x00007fa4e030a200>

INCHI for #<Metabolite:0x00007fa4e030a200>

Structure for #<Metabolite:0x00007fa4e030a200>

3D Structure for #<Metabolite:0x00007fa4e030a200>