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Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References enzymes (16) Show 16 proteins XML

Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2019-04-04 16:06:50 UTC

Update Date

2022-09-22 17:44:59 UTC

HMDB ID

HMDB0240328

Secondary Accession Numbers

None

Metabolite Identification

Common Name

2'-O-Methyluridine

Description

2'-O-Methyluridine 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. 2'-O-Methyluridine was identified as one of forty plasma metabolites that could be used to predict gut microbiome Shannon diversity (PMID: 31477923 ). Shannon diversity is a metric that summarizes both species abundance and evenness, and it has been suggested as a marker for microbiome health.

Structure

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

HMDB0240328
     RDKit          3D
2'-O-Methyluridine
 32 33  0  0  0  0  0  0  0  0999 V2000
   -1.7126    2.9934    0.6355 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7061    1.6061    0.6869 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6556    1.0703   -0.0874 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.3380    0.1175   -1.0587 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.4219    0.7082   -1.6846 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7573   -0.9232   -0.0390 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.3031   -2.1613   -0.6866 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5540   -3.1459    0.2580 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5687   -1.1462    0.6368 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0653    0.0917    0.7621 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4518   -0.0974    0.4758 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0475    0.2780   -0.6612 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3823    0.0875   -0.9186 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1277   -0.5359    0.0855 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3448   -0.7284   -0.1072 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5034   -0.9017    1.2159 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1936   -0.7056    1.4479 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6988   -1.0817    2.5351 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7796    3.4066    1.0148 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8927    3.2575   -0.4458 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6207    3.3261    1.1792 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0612    1.8364   -0.5688 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6492   -0.3668   -1.7502 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3252    0.5197   -2.6573 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4668   -0.4569    0.6681 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6888   -2.4905   -1.5325 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3024   -1.8838   -1.1167 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4066   -2.8307    1.1729 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0145    0.3772    1.8488 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4419    0.7552   -1.4124 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8668    0.3912   -1.8396 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1013   -1.3667    1.9433 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  4  6  1  0
  6  7  1  0
  7  8  1  0
  6  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
 14 15  2  0
 14 16  1  0
 16 17  1  0
 17 18  2  0
 10  3  1  0
 17 11  1  0
  1 19  1  0
  1 20  1  0
  1 21  1  0
  3 22  1  6
  4 23  1  6
  5 24  1  0
  6 25  1  1
  7 26  1  0
  7 27  1  0
  8 28  1  0
 10 29  1  1
 12 30  1  0
 13 31  1  0
 16 32  1  0
M  END


  Mrv1652302032022552D          

 18 19  0  0  1  0            999 V2000
   14.2805   -6.3537    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   14.2805   -5.5287    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   13.6130   -6.8388    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.9480   -6.8388    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   14.9949   -5.1162    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.5661   -5.1162    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.8680   -7.6233    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   14.6930   -7.6233    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   15.7325   -6.5837    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.9949   -4.2912    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   15.1780   -8.2908    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.2805   -3.8787    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.3831   -8.2908    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.7187   -9.0444    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.2805   -3.0537    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.7095   -5.5287    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.5661   -4.2912    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.3457   -7.1357    0.0000 C   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 16  2  0  0  0  0
  6 17  2  0  0  0  0
  7 13  1  1  0  0  0
  8 11  1  6  0  0  0
 10 12  1  0  0  0  0
 12 15  2  0  0  0  0
  7  8  1  0  0  0  0
 17 12  1  0  0  0  0
 13 14  1  0  0  0  0
  9 18  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0240328

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C10H14N2O6/c1-17-8-7(15)5(4-13)18-9(8)12-3-2-6(14)11-10(12)16/h2-3,5,7-9,13,15H,4H2,1H3,(H,11,14,16)/t5-,7-,8-,9-/m1/s1

> <INCHI_KEY>
SXUXMRMBWZCMEN-ZOQUXTDFSA-N

> <FORMULA>
C10H14N2O6

> <MOLECULAR_WEIGHT>
258.23

> <EXACT_MASS>
258.085186179

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
32

> <JCHEM_AVERAGE_POLARIZABILITY>
23.912906995172523

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1-[(2R,3R,4R,5R)-4-hydroxy-5-(hydroxymethyl)-3-methoxyoxolan-2-yl]-1,2,3,4-tetrahydropyrimidine-2,4-dione

> <ALOGPS_LOGP>
-1.37

> <JCHEM_LOGP>
-1.7721156379999996

> <ALOGPS_LOGS>
-0.38

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.0181255742317

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.701117533854916

> <JCHEM_PKA_STRONGEST_BASIC>
-2.980305724013834

> <JCHEM_POLAR_SURFACE_AREA>
108.33000000000001

> <JCHEM_REFRACTIVITY>
57.31680000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.08e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1-[(2R,3R,4R,5R)-4-hydroxy-5-(hydroxymethyl)-3-methoxyoxolan-2-yl]-3H-pyrimidine-2,4-dione

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0240328
     RDKit          3D
2'-O-Methyluridine
 32 33  0  0  0  0  0  0  0  0999 V2000
   -1.7126    2.9934    0.6355 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7061    1.6061    0.6869 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6556    1.0703   -0.0874 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.3380    0.1175   -1.0587 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.4219    0.7082   -1.6846 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7573   -0.9232   -0.0390 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.3031   -2.1613   -0.6866 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5540   -3.1459    0.2580 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5687   -1.1462    0.6368 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0653    0.0917    0.7621 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4518   -0.0974    0.4758 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0475    0.2780   -0.6612 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3823    0.0875   -0.9186 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1277   -0.5359    0.0855 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3448   -0.7284   -0.1072 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5034   -0.9017    1.2159 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1936   -0.7056    1.4479 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6988   -1.0817    2.5351 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7796    3.4066    1.0148 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8927    3.2575   -0.4458 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6207    3.3261    1.1792 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0612    1.8364   -0.5688 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6492   -0.3668   -1.7502 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3252    0.5197   -2.6573 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4668   -0.4569    0.6681 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6888   -2.4905   -1.5325 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3024   -1.8838   -1.1167 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4066   -2.8307    1.1729 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0145    0.3772    1.8488 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4419    0.7552   -1.4124 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8668    0.3912   -1.8396 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1013   -1.3667    1.9433 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  4  6  1  0
  6  7  1  0
  7  8  1  0
  6  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
 14 15  2  0
 14 16  1  0
 16 17  1  0
 17 18  2  0
 10  3  1  0
 17 11  1  0
  1 19  1  0
  1 20  1  0
  1 21  1  0
  3 22  1  6
  4 23  1  6
  5 24  1  0
  6 25  1  1
  7 26  1  0
  7 27  1  0
  8 28  1  0
 10 29  1  1
 12 30  1  0
 13 31  1  0
 16 32  1  0
M  END

HEADER    PROTEIN                                 03-FEB-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-FEB-20         0                                  
HETATM    1  C   UNK     0      26.657 -11.860   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0      26.657 -10.320   0.000  0.00  0.00           N+0
HETATM    3  O   UNK     0      25.411 -12.766   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      27.903 -12.766   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      27.990  -9.550   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      25.323  -9.550   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      25.887 -14.230   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      27.427 -14.230   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      29.367 -12.290   0.000  0.00  0.00           O+0
HETATM   10  N   UNK     0      27.990  -8.010   0.000  0.00  0.00           N+0
HETATM   11  O   UNK     0      28.332 -15.476   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      26.657  -7.240   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      24.982 -15.476   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      25.608 -16.883   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0      26.657  -5.700   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0      29.324 -10.320   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0      25.323  -8.010   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      30.512 -13.320   0.000  0.00  0.00           C+0
CONECT    1    2    3    4                                                  
CONECT    2    1    5    6                                                  
CONECT    3    1    7                                                       
CONECT    4    1    8    9                                                  
CONECT    5    2   10   16                                                  
CONECT    6    2   17                                                       
CONECT    7    3   13    8                                                  
CONECT    8    4   11    7                                                  
CONECT    9    4   18                                                       
CONECT   10    5   12                                                       
CONECT   11    8                                                            
CONECT   12   10   15   17                                                  
CONECT   13    7   14                                                       
CONECT   14   13                                                            
CONECT   15   12                                                            
CONECT   16    5                                                            
CONECT   17    6   12                                                       
CONECT   18    9                                                            
MASTER        0    0    0    0    0    0    0    0   18    0   38    0
END

COMPND    HMDB0240328
HETATM    1  C1  UNL     1      -1.713   2.993   0.635  1.00  0.00           C  
HETATM    2  O1  UNL     1      -1.706   1.606   0.687  1.00  0.00           O  
HETATM    3  C2  UNL     1      -0.656   1.070  -0.087  1.00  0.00           C  
HETATM    4  C3  UNL     1      -1.338   0.118  -1.059  1.00  0.00           C  
HETATM    5  O2  UNL     1      -2.422   0.708  -1.685  1.00  0.00           O  
HETATM    6  C4  UNL     1      -1.757  -0.923  -0.039  1.00  0.00           C  
HETATM    7  C5  UNL     1      -2.303  -2.161  -0.687  1.00  0.00           C  
HETATM    8  O3  UNL     1      -2.554  -3.146   0.258  1.00  0.00           O  
HETATM    9  O4  UNL     1      -0.569  -1.146   0.637  1.00  0.00           O  
HETATM   10  C6  UNL     1       0.065   0.092   0.762  1.00  0.00           C  
HETATM   11  N1  UNL     1       1.452  -0.097   0.476  1.00  0.00           N  
HETATM   12  C7  UNL     1       2.047   0.278  -0.661  1.00  0.00           C  
HETATM   13  C8  UNL     1       3.382   0.088  -0.919  1.00  0.00           C  
HETATM   14  C9  UNL     1       4.128  -0.536   0.086  1.00  0.00           C  
HETATM   15  O5  UNL     1       5.345  -0.728  -0.107  1.00  0.00           O  
HETATM   16  N2  UNL     1       3.503  -0.902   1.216  1.00  0.00           N  
HETATM   17  C10 UNL     1       2.194  -0.706   1.448  1.00  0.00           C  
HETATM   18  O6  UNL     1       1.699  -1.082   2.535  1.00  0.00           O  
HETATM   19  H1  UNL     1      -0.780   3.407   1.015  1.00  0.00           H  
HETATM   20  H2  UNL     1      -1.893   3.257  -0.446  1.00  0.00           H  
HETATM   21  H3  UNL     1      -2.621   3.326   1.179  1.00  0.00           H  
HETATM   22  H4  UNL     1      -0.061   1.836  -0.569  1.00  0.00           H  
HETATM   23  H5  UNL     1      -0.649  -0.367  -1.750  1.00  0.00           H  
HETATM   24  H6  UNL     1      -2.325   0.520  -2.657  1.00  0.00           H  
HETATM   25  H7  UNL     1      -2.467  -0.457   0.668  1.00  0.00           H  
HETATM   26  H8  UNL     1      -1.689  -2.491  -1.533  1.00  0.00           H  
HETATM   27  H9  UNL     1      -3.302  -1.884  -1.117  1.00  0.00           H  
HETATM   28  H10 UNL     1      -2.407  -2.831   1.173  1.00  0.00           H  
HETATM   29  H11 UNL     1      -0.014   0.377   1.849  1.00  0.00           H  
HETATM   30  H12 UNL     1       1.442   0.755  -1.412  1.00  0.00           H  
HETATM   31  H13 UNL     1       3.867   0.391  -1.840  1.00  0.00           H  
HETATM   32  H14 UNL     1       4.101  -1.367   1.943  1.00  0.00           H  
CONECT    1    2   19   20   21
CONECT    2    3
CONECT    3    4   10   22
CONECT    4    5    6   23
CONECT    5   24
CONECT    6    7    9   25
CONECT    7    8   26   27
CONECT    8   28
CONECT    9   10
CONECT   10   11   29
CONECT   11   12   17
CONECT   12   13   13   30
CONECT   13   14   31
CONECT   14   15   15   16
CONECT   16   17   32
CONECT   17   18   18
END

HMDB0240328
     RDKit          3D
2'-O-Methyluridine
 32 33  0  0  0  0  0  0  0  0999 V2000
   -1.7126    2.9934    0.6355 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7061    1.6061    0.6869 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6556    1.0703   -0.0874 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.3380    0.1175   -1.0587 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.4219    0.7082   -1.6846 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7573   -0.9232   -0.0390 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.3031   -2.1613   -0.6866 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5540   -3.1459    0.2580 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5687   -1.1462    0.6368 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0653    0.0917    0.7621 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4518   -0.0974    0.4758 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0475    0.2780   -0.6612 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3823    0.0875   -0.9186 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1277   -0.5359    0.0855 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3448   -0.7284   -0.1072 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5034   -0.9017    1.2159 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1936   -0.7056    1.4479 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6988   -1.0817    2.5351 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7796    3.4066    1.0148 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8927    3.2575   -0.4458 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6207    3.3261    1.1792 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0612    1.8364   -0.5688 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6492   -0.3668   -1.7502 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3252    0.5197   -2.6573 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4668   -0.4569    0.6681 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6888   -2.4905   -1.5325 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3024   -1.8838   -1.1167 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4066   -2.8307    1.1729 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0145    0.3772    1.8488 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4419    0.7552   -1.4124 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8668    0.3912   -1.8396 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1013   -1.3667    1.9433 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  4  6  1  0
  6  7  1  0
  7  8  1  0
  6  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
 14 15  2  0
 14 16  1  0
 16 17  1  0
 17 18  2  0
 10  3  1  0
 17 11  1  0
  1 19  1  0
  1 20  1  0
  1 21  1  0
  3 22  1  6
  4 23  1  6
  5 24  1  0
  6 25  1  1
  7 26  1  0
  7 27  1  0
  8 28  1  0
 10 29  1  1
 12 30  1  0
 13 31  1  0
 16 32  1  0
M  END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
O(2')-Methyluridine	ChEBI
um	ChEBI
2’-O-methyluridine	HMDB
O-Methyluridine	HMDB
2'-O-Methyluridine	HMDB

Chemical Formula

C₁₀H₁₄N₂O₆

Average Molecular Weight

258.23

Monoisotopic Molecular Weight

258.085186179

IUPAC Name

1-[(2R,3R,4R,5R)-4-hydroxy-5-(hydroxymethyl)-3-methoxyoxolan-2-yl]-1,2,3,4-tetrahydropyrimidine-2,4-dione

Traditional Name

1-[(2R,3R,4R,5R)-4-hydroxy-5-(hydroxymethyl)-3-methoxyoxolan-2-yl]-3H-pyrimidine-2,4-dione

CAS Registry Number

2140-76-3

SMILES

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

InChI Identifier

InChI=1S/C10H14N2O6/c1-17-8-7(15)5(4-13)18-9(8)12-3-2-6(14)11-10(12)16/h2-3,5,7-9,13,15H,4H2,1H3,(H,11,14,16)/t5-,7-,8-,9-/m1/s1

InChI Key

SXUXMRMBWZCMEN-ZOQUXTDFSA-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
Pyrimidone
Hydroxypyrimidine
Hydropyrimidine
Monosaccharide
Pyrimidine
Tetrahydrofuran
Heteroaromatic compound
Secondary alcohol
Azacycle
Organoheterocyclic compound
Dialkyl ether
Oxacycle
Ether
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Alcohol
Organic oxygen compound
Organic nitrogen compound
Primary alcohol
Organopnictogen compound
Organic oxide
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

methyluridine (CHEBI:19227 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 31477923)

Excreta

Biofluid or Excreta

Feces (PMID: 29808030)

Source

Exogenous

Exogenous (HMDB: HMDB0240328)

Process

Not Available

Role

Not Available

Physical Properties

State

Not Available

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
logP	-1.4	ALOGPS
logP	-1.8	ChemAxon
logS	-0.38	ALOGPS
pKa (Strongest Acidic)	9.7	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	108.33 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	57.32 m³·mol⁻¹	ChemAxon
Polarizability	23.91 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
DeepCCS	[M+H]+	163.693	30932474
DeepCCS	[M-H]-	161.323	30932474
DeepCCS	[M-2H]-	194.93	30932474
DeepCCS	[M+Na]+	170.156	30932474
AllCCS	[M+H]+	158.1	32859911
AllCCS	[M+H-H2O]+	154.5	32859911
AllCCS	[M+NH4]+	161.6	32859911
AllCCS	[M+Na]+	162.5	32859911
AllCCS	[M-H]-	156.6	32859911
AllCCS	[M+Na-2H]-	156.6	32859911
AllCCS	[M+HCOO]-	156.7	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
2'-O-Methyluridine	CO[C@@H]1[C@H](O)[C@@H](CO)O[C@H]1N1C=CC(=O)NC1=O	3241.2	Standard polar	33892256
2'-O-Methyluridine	CO[C@@H]1[C@H](O)[C@@H](CO)O[C@H]1N1C=CC(=O)NC1=O	2146.5	Standard non polar	33892256
2'-O-Methyluridine	CO[C@@H]1[C@H](O)[C@@H](CO)O[C@H]1N1C=CC(=O)NC1=O	2451.5	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
2'-O-Methyluridine,1TMS,isomer #1	CO[C@@H]1[C@H](O[Si](C)(C)C)[C@@H](CO)O[C@H]1N1C=CC(=O)[NH]C1=O	2297.4	Semi standard non polar	33892256
2'-O-Methyluridine,1TMS,isomer #2	CO[C@@H]1[C@H](O)[C@@H](CO[Si](C)(C)C)O[C@H]1N1C=CC(=O)[NH]C1=O	2279.6	Semi standard non polar	33892256
2'-O-Methyluridine,1TMS,isomer #3	CO[C@@H]1[C@H](O)[C@@H](CO)O[C@H]1N1C=CC(=O)N([Si](C)(C)C)C1=O	2331.5	Semi standard non polar	33892256
2'-O-Methyluridine,2TMS,isomer #1	CO[C@@H]1[C@H](O[Si](C)(C)C)[C@@H](CO[Si](C)(C)C)O[C@H]1N1C=CC(=O)[NH]C1=O	2283.3	Semi standard non polar	33892256
2'-O-Methyluridine,2TMS,isomer #2	CO[C@@H]1[C@H](O[Si](C)(C)C)[C@@H](CO)O[C@H]1N1C=CC(=O)N([Si](C)(C)C)C1=O	2356.5	Semi standard non polar	33892256
2'-O-Methyluridine,2TMS,isomer #3	CO[C@@H]1[C@H](O)[C@@H](CO[Si](C)(C)C)O[C@H]1N1C=CC(=O)N([Si](C)(C)C)C1=O	2365.6	Semi standard non polar	33892256
2'-O-Methyluridine,3TMS,isomer #1	CO[C@@H]1[C@H](O[Si](C)(C)C)[C@@H](CO[Si](C)(C)C)O[C@H]1N1C=CC(=O)N([Si](C)(C)C)C1=O	2387.7	Semi standard non polar	33892256
2'-O-Methyluridine,3TMS,isomer #1	CO[C@@H]1[C@H](O[Si](C)(C)C)[C@@H](CO[Si](C)(C)C)O[C@H]1N1C=CC(=O)N([Si](C)(C)C)C1=O	2574.1	Standard non polar	33892256
2'-O-Methyluridine,3TMS,isomer #1	CO[C@@H]1[C@H](O[Si](C)(C)C)[C@@H](CO[Si](C)(C)C)O[C@H]1N1C=CC(=O)N([Si](C)(C)C)C1=O	2623.2	Standard polar	33892256
2'-O-Methyluridine,1TBDMS,isomer #1	CO[C@@H]1[C@H](O[Si](C)(C)C(C)(C)C)[C@@H](CO)O[C@H]1N1C=CC(=O)[NH]C1=O	2514.6	Semi standard non polar	33892256
2'-O-Methyluridine,1TBDMS,isomer #2	CO[C@@H]1[C@H](O)[C@@H](CO[Si](C)(C)C(C)(C)C)O[C@H]1N1C=CC(=O)[NH]C1=O	2524.9	Semi standard non polar	33892256
2'-O-Methyluridine,1TBDMS,isomer #3	CO[C@@H]1[C@H](O)[C@@H](CO)O[C@H]1N1C=CC(=O)N([Si](C)(C)C(C)(C)C)C1=O	2566.5	Semi standard non polar	33892256
2'-O-Methyluridine,2TBDMS,isomer #1	CO[C@@H]1[C@H](O[Si](C)(C)C(C)(C)C)[C@@H](CO[Si](C)(C)C(C)(C)C)O[C@H]1N1C=CC(=O)[NH]C1=O	2731.6	Semi standard non polar	33892256
2'-O-Methyluridine,2TBDMS,isomer #2	CO[C@@H]1[C@H](O[Si](C)(C)C(C)(C)C)[C@@H](CO)O[C@H]1N1C=CC(=O)N([Si](C)(C)C(C)(C)C)C1=O	2796.0	Semi standard non polar	33892256
2'-O-Methyluridine,2TBDMS,isomer #3	CO[C@@H]1[C@H](O)[C@@H](CO[Si](C)(C)C(C)(C)C)O[C@H]1N1C=CC(=O)N([Si](C)(C)C(C)(C)C)C1=O	2803.1	Semi standard non polar	33892256
2'-O-Methyluridine,3TBDMS,isomer #1	CO[C@@H]1[C@H](O[Si](C)(C)C(C)(C)C)[C@@H](CO[Si](C)(C)C(C)(C)C)O[C@H]1N1C=CC(=O)N([Si](C)(C)C(C)(C)C)C1=O	3012.1	Semi standard non polar	33892256
2'-O-Methyluridine,3TBDMS,isomer #1	CO[C@@H]1[C@H](O[Si](C)(C)C(C)(C)C)[C@@H](CO[Si](C)(C)C(C)(C)C)O[C@H]1N1C=CC(=O)N([Si](C)(C)C(C)(C)C)C1=O	3139.9	Standard non polar	33892256
2'-O-Methyluridine,3TBDMS,isomer #1	CO[C@@H]1[C@H](O[Si](C)(C)C(C)(C)C)[C@@H](CO[Si](C)(C)C(C)(C)C)O[C@H]1N1C=CC(=O)N([Si](C)(C)C(C)(C)C)C1=O	2946.6	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - 2'-O-Methyluridine GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Experimental LC-MS/MS	LC-MS/MS Spectrum - 2'-O-Methyluridine 35V, Negative-QTOF	splash10-01ox-8190000000-04836f429bee6438aec5	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 2'-O-Methyluridine 35V, Positive-QTOF	splash10-004i-0900000000-a95dcd4a4fad1b7c10a4	2021-09-20	HMDB team, MONA	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2'-O-Methyluridine 10V, Negative-QTOF	splash10-03di-2920000000-ab0a3d06c2a5fab92522	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2'-O-Methyluridine 20V, Negative-QTOF	splash10-01ox-9700000000-2ea5d2f1349adb3f0aff	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2'-O-Methyluridine 40V, Negative-QTOF	splash10-0006-9100000000-a6372c939a9cb283f774	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2'-O-Methyluridine 10V, Positive-QTOF	splash10-0400-0910000000-90907a6ba444cc94d805	2021-09-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2'-O-Methyluridine 20V, Positive-QTOF	splash10-03di-5900000000-dbfce876c5243b99fa59	2021-09-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2'-O-Methyluridine 40V, Positive-QTOF	splash10-0296-9300000000-d997d0b3fefede5e7b64	2021-09-21	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood
Feces
Urine

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	31477923	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	29808030	details
Urine	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	34436864	details

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

92343

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

102212

PDB ID

Not Available

ChEBI ID

19227

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Wilmanski T, Rappaport N, Earls JC, Magis AT, Manor O, Lovejoy J, Omenn GS, Hood L, Gibbons SM, Price ND: Blood metabolome predicts gut microbiome alpha-diversity in humans. Nat Biotechnol. 2019 Oct;37(10):1217-1228. doi: 10.1038/s41587-019-0233-9. Epub 2019 Sep 2. [PubMed:31477923 ]

Only showing the first 10 proteins. There are 16 proteins in total.

Show all enzymes and transporters

Enzymes

Enzyme Details

1. Putative ribosomal RNA methyltransferase 2

General function:: Involved in methyltransferase activity
Specific function:: Probable methyltransferase.
Gene Name:: FTSJ2
Uniprot ID:: Q9UI43
Molecular weight:: 27423.365

Enzyme Details

2. Probable tRNA (uracil-O(2)-)-methyltransferase

General function:: Not Available
Specific function:: Probable adenosyl-L-methionine (AdoMet)-dependent tRNA (uracil-O(2)-)-methyltransferase (By similarity).
Gene Name:: TRMT44
Uniprot ID:: Q8IYL2
Molecular weight:: 84628.16

Enzyme Details

3. Ribosomal RNA large subunit methyltransferase E

General function:: Not Available
Specific function:: Specifically methylates the uridine in position 2552 of 23S rRNA at the 2'-O position of the ribose in the fully assembled 50S ribosomal subunit.
Gene Name:: RLME
Uniprot ID:: Q2NHD6
Molecular weight:: 23393.735

Enzyme Details

4. Ribosomal RNA large subunit methyltransferase E

General function:: Not Available
Specific function:: Specifically methylates the uridine in position 2552 of 23S rRNA at the 2'-O position of the ribose in the fully assembled 50S ribosomal subunit.
Gene Name:: RLME
Uniprot ID:: A1AG82
Molecular weight:: 23334.92

Enzyme Details

5. Ribosomal RNA large subunit methyltransferase E

General function:: Not Available
Specific function:: Specifically methylates the uridine in position 2552 of 23S rRNA at the 2'-O position of the ribose in the fully assembled 50S ribosomal subunit.
Gene Name:: RLME
Uniprot ID:: Q2GGT6
Molecular weight:: 24373.735

Enzyme Details

6. Ribosomal RNA large subunit methyltransferase E

General function:: Not Available
Specific function:: Specifically methylates the uridine in position 2552 of 23S rRNA at the 2'-O position of the ribose in the fully assembled 50S ribosomal subunit.
Gene Name:: RLME
Uniprot ID:: Q2GDL7
Molecular weight:: 24052.61

Enzyme Details

7. Ribosomal RNA large subunit methyltransferase E

General function:: Not Available
Specific function:: Specifically methylates the uridine in position 2552 of 23S rRNA at the 2'-O position of the ribose in the fully assembled 50S ribosomal subunit.
Gene Name:: RLME
Uniprot ID:: Q6G0S9
Molecular weight:: 26685.75

Enzyme Details

8. Ribosomal RNA large subunit methyltransferase E

General function:: Not Available
Specific function:: Specifically methylates the uridine in position 2552 of 23S rRNA at the 2'-O position of the ribose in the fully assembled 50S ribosomal subunit.
Gene Name:: RLME
Uniprot ID:: Q6G4Z3
Molecular weight:: 27322.35

Enzyme Details

9. Ribosomal RNA large subunit methyltransferase E

General function:: Not Available
Specific function:: Specifically methylates the uridine in position 2552 of 23S rRNA at the 2'-O position of the ribose in the fully assembled 50S ribosomal subunit.
Gene Name:: RLME
Uniprot ID:: Q5PLC1
Molecular weight:: 23251.825

Enzyme Details

10. Ribosomal RNA large subunit methyltransferase E

General function:: Not Available
Specific function:: Specifically methylates the uridine in position 2552 of 23S rRNA at the 2'-O position of the ribose in the fully assembled 50S ribosomal subunit.
Gene Name:: RLME
Uniprot ID:: Q0BT08
Molecular weight:: 24550.145

Only showing the first 10 proteins. There are 16 proteins in total.

Show all enzymes and transporters

Showing metabocard for 2'-O-Methyluridine (HMDB0240328)

MOL for HMDB0240328 (2'-O-Methyluridine)

3D MOL for HMDB0240328 (2'-O-Methyluridine)

3D SDF for HMDB0240328 (2'-O-Methyluridine)

3D-SDF for HMDB0240328 (2'-O-Methyluridine)

PDB for HMDB0240328 (2'-O-Methyluridine)

3D PDB for HMDB0240328 (2'-O-Methyluridine)

SMILES for HMDB0240328 (2'-O-Methyluridine)

INCHI for HMDB0240328 (2'-O-Methyluridine)

Structure for HMDB0240328 (2'-O-Methyluridine)

3D Structure for HMDB0240328 (2'-O-Methyluridine)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

Enzymes