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Record Information

Version

5.0

Status

Detected and Quantified

Creation Date

2006-08-24 11:48:54 UTC

Update Date

2021-09-14 15:47:57 UTC

HMDB ID

HMDB0004813

Secondary Accession Numbers

HMDB04813

Metabolite Identification

Common Name

3-Methyluridine

Description

3-Methyluridine is a modified nucleoside of cellular RNA. All modifications are formed post-transcriptionally in RNA from the normal nucleosides by modifying enzymes, especially specific RNA-methyltransferases and RNA-synthetases. Due to the lack of specific phosphorylases for modified nucleosides they cannot be recycled for synthesizing RNA, so they are excreted quantitatively in urine. (PMID 15906010 ).

Structure

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

HMDB0004813
     RDKit          3D
3-Methyluridine
 32 33  0  0  0  0  0  0  0  0999 V2000
    4.3899   -0.1557    1.0310 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2601    0.1970    0.1729 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.4429    0.7466   -1.0359 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6183    0.9585   -1.4290 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3335    1.0539   -1.7918 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0575    0.7851   -1.2789 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9138    0.2342   -0.0647 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3805   -0.0446    0.4691 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3278    0.9007    0.1879 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5490    0.3127    0.0379 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5265    0.8706    1.0470 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6402    2.2379    0.8395 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4075   -1.1662    0.3190 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2322   -1.9291   -0.5105 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9395   -1.3740   -0.0292 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8639   -1.4710   -1.4167 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0207   -0.0481    0.6354 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9030   -0.5645    1.7747 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0607   -0.1686    2.0866 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1940    0.6169    0.8865 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7663   -1.1398    0.6879 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4824    1.4937   -2.7589 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1941    1.0297   -1.8792 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3482   -0.1520    1.5934 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9722    0.4937   -0.9594 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5302    0.4239    0.8921 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1873    0.7300    2.0909 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1425    2.5373    0.0562 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6031   -1.3502    1.3847 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8585   -2.8221   -0.6296 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4955   -2.2311    0.4778 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6327   -1.0057   -1.8677 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  3  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 10 13  1  0
 13 14  1  0
 13 15  1  0
 15 16  1  0
  7 17  1  0
 17 18  2  0
 17  2  1  0
 15  8  1  0
  1 19  1  0
  1 20  1  0
  1 21  1  0
  5 22  1  0
  6 23  1  0
  8 24  1  0
 10 25  1  0
 11 26  1  0
 11 27  1  0
 12 28  1  0
 13 29  1  0
 14 30  1  0
 15 31  1  0
 16 32  1  0
M  END


  Mrv0541 02231219592D          

 18 19  0  0  0  0            999 V2000
   19.7620  -14.6102    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.5920  -12.9894    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.1466  -14.6965    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.7115  -13.2445    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.6152  -11.9345    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.0441   -9.4595    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.3296  -10.6970    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   18.0441  -11.9345    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   18.9415  -14.6965    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.6152  -10.2845    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.0441  -12.7595    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.4566  -14.0290    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.3767  -13.2445    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.6316  -14.0290    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.3296  -11.5220    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.0441  -10.2845    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.7585  -11.5220    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.7585  -10.6970    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  9  1  0  0  0  0
  2 13  1  0  0  0  0
  3 14  1  0  0  0  0
  4 11  1  0  0  0  0
  4 12  1  0  0  0  0
  5 15  2  0  0  0  0
  6 16  2  0  0  0  0
  7 10  1  0  0  0  0
  7 15  1  0  0  0  0
  7 16  1  0  0  0  0
  8 11  1  0  0  0  0
  8 15  1  0  0  0  0
  8 17  1  0  0  0  0
  9 12  1  0  0  0  0
 11 13  1  0  0  0  0
 12 14  1  0  0  0  0
 13 14  1  0  0  0  0
 16 18  1  0  0  0  0
 17 18  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0004813

> <DATABASE_NAME>
hmdb

> <SMILES>
CN1C(=O)C=CN(C2OC(CO)C(O)C2O)C1=O

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

> <INCHI_KEY>
UTQUILVPBZEHTK-UHFFFAOYSA-N

> <FORMULA>
C10H14N2O6

> <MOLECULAR_WEIGHT>
258.228

> <EXACT_MASS>
258.08518619

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_AVERAGE_POLARIZABILITY>
24.208394780225664

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-1.43

> <JCHEM_LOGP>
-2.1915660759999995

> <ALOGPS_LOGS>
-0.00

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.933964639655862

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.55383181284234

> <JCHEM_PKA_STRONGEST_BASIC>
-2.980299639602592

> <JCHEM_POLAR_SURFACE_AREA>
110.53999999999999

> <JCHEM_REFRACTIVITY>
57.462299999999985

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.57e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
N-3-methyluridine

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0004813
     RDKit          3D
3-Methyluridine
 32 33  0  0  0  0  0  0  0  0999 V2000
    4.3899   -0.1557    1.0310 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2601    0.1970    0.1729 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.4429    0.7466   -1.0359 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6183    0.9585   -1.4290 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3335    1.0539   -1.7918 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0575    0.7851   -1.2789 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9138    0.2342   -0.0647 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3805   -0.0446    0.4691 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3278    0.9007    0.1879 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5490    0.3127    0.0379 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5265    0.8706    1.0470 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6402    2.2379    0.8395 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4075   -1.1662    0.3190 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2322   -1.9291   -0.5105 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9395   -1.3740   -0.0292 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8639   -1.4710   -1.4167 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0207   -0.0481    0.6354 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9030   -0.5645    1.7747 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0607   -0.1686    2.0866 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1940    0.6169    0.8865 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7663   -1.1398    0.6879 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4824    1.4937   -2.7589 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1941    1.0297   -1.8792 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3482   -0.1520    1.5934 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9722    0.4937   -0.9594 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5302    0.4239    0.8921 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1873    0.7300    2.0909 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1425    2.5373    0.0562 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6031   -1.3502    1.3847 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8585   -2.8221   -0.6296 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4955   -2.2311    0.4778 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6327   -1.0057   -1.8677 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  3  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 10 13  1  0
 13 14  1  0
 13 15  1  0
 15 16  1  0
  7 17  1  0
 17 18  2  0
 17  2  1  0
 15  8  1  0
  1 19  1  0
  1 20  1  0
  1 21  1  0
  5 22  1  0
  6 23  1  0
  8 24  1  0
 10 25  1  0
 11 26  1  0
 11 27  1  0
 12 28  1  0
 13 29  1  0
 14 30  1  0
 15 31  1  0
 16 32  1  0
M  END

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  O   UNK     0      36.889 -27.272   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      30.972 -24.247   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      32.007 -27.433   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      34.928 -24.723   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0      31.015 -22.278   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0      33.682 -17.658   0.000  0.00  0.00           O+0
HETATM    7  N   UNK     0      32.349 -19.968   0.000  0.00  0.00           N+0
HETATM    8  N   UNK     0      33.682 -22.278   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0      35.357 -27.433   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      31.015 -19.198   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      33.682 -23.818   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      34.452 -26.187   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      32.437 -24.723   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      32.912 -26.187   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      32.349 -21.508   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      33.682 -19.198   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      35.016 -21.508   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      35.016 -19.968   0.000  0.00  0.00           C+0
CONECT    1    9                                                            
CONECT    2   13                                                            
CONECT    3   14                                                            
CONECT    4   11   12                                                       
CONECT    5   15                                                            
CONECT    6   16                                                            
CONECT    7   10   15   16                                                  
CONECT    8   11   15   17                                                  
CONECT    9    1   12                                                       
CONECT   10    7                                                            
CONECT   11    4    8   13                                                  
CONECT   12    4    9   14                                                  
CONECT   13    2   11   14                                                  
CONECT   14    3   12   13                                                  
CONECT   15    5    7    8                                                  
CONECT   16    6    7   18                                                  
CONECT   17    8   18                                                       
CONECT   18   16   17                                                       
MASTER        0    0    0    0    0    0    0    0   18    0   38    0
END

COMPND    HMDB0004813
HETATM    1  C1  UNL     1       4.390  -0.156   1.031  1.00  0.00           C  
HETATM    2  N1  UNL     1       3.260   0.197   0.173  1.00  0.00           N  
HETATM    3  C2  UNL     1       3.443   0.747  -1.036  1.00  0.00           C  
HETATM    4  O1  UNL     1       4.618   0.959  -1.429  1.00  0.00           O  
HETATM    5  C3  UNL     1       2.334   1.054  -1.792  1.00  0.00           C  
HETATM    6  C4  UNL     1       1.058   0.785  -1.279  1.00  0.00           C  
HETATM    7  N2  UNL     1       0.914   0.234  -0.065  1.00  0.00           N  
HETATM    8  C5  UNL     1      -0.380  -0.045   0.469  1.00  0.00           C  
HETATM    9  O2  UNL     1      -1.328   0.901   0.188  1.00  0.00           O  
HETATM   10  C6  UNL     1      -2.549   0.313   0.038  1.00  0.00           C  
HETATM   11  C7  UNL     1      -3.526   0.871   1.047  1.00  0.00           C  
HETATM   12  O3  UNL     1      -3.640   2.238   0.839  1.00  0.00           O  
HETATM   13  C8  UNL     1      -2.408  -1.166   0.319  1.00  0.00           C  
HETATM   14  O4  UNL     1      -3.232  -1.929  -0.510  1.00  0.00           O  
HETATM   15  C9  UNL     1      -0.940  -1.374  -0.029  1.00  0.00           C  
HETATM   16  O5  UNL     1      -0.864  -1.471  -1.417  1.00  0.00           O  
HETATM   17  C10 UNL     1       2.021  -0.048   0.635  1.00  0.00           C  
HETATM   18  O6  UNL     1       1.903  -0.564   1.775  1.00  0.00           O  
HETATM   19  H1  UNL     1       4.061  -0.169   2.087  1.00  0.00           H  
HETATM   20  H2  UNL     1       5.194   0.617   0.886  1.00  0.00           H  
HETATM   21  H3  UNL     1       4.766  -1.140   0.688  1.00  0.00           H  
HETATM   22  H4  UNL     1       2.482   1.494  -2.759  1.00  0.00           H  
HETATM   23  H5  UNL     1       0.194   1.030  -1.879  1.00  0.00           H  
HETATM   24  H6  UNL     1      -0.348  -0.152   1.593  1.00  0.00           H  
HETATM   25  H7  UNL     1      -2.972   0.494  -0.959  1.00  0.00           H  
HETATM   26  H8  UNL     1      -4.530   0.424   0.892  1.00  0.00           H  
HETATM   27  H9  UNL     1      -3.187   0.730   2.091  1.00  0.00           H  
HETATM   28  H10 UNL     1      -3.142   2.537   0.056  1.00  0.00           H  
HETATM   29  H11 UNL     1      -2.603  -1.350   1.385  1.00  0.00           H  
HETATM   30  H12 UNL     1      -2.858  -2.822  -0.630  1.00  0.00           H  
HETATM   31  H13 UNL     1      -0.496  -2.231   0.478  1.00  0.00           H  
HETATM   32  H14 UNL     1      -1.633  -1.006  -1.868  1.00  0.00           H  
CONECT    1    2   19   20   21
CONECT    2    3   17
CONECT    3    4    4    5
CONECT    5    6    6   22
CONECT    6    7   23
CONECT    7    8   17
CONECT    8    9   15   24
CONECT    9   10
CONECT   10   11   13   25
CONECT   11   12   26   27
CONECT   12   28
CONECT   13   14   15   29
CONECT   14   30
CONECT   15   16   31
CONECT   16   32
CONECT   17   18   18
END

HMDB0004813
     RDKit          3D
3-Methyluridine
 32 33  0  0  0  0  0  0  0  0999 V2000
    4.3899   -0.1557    1.0310 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2601    0.1970    0.1729 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.4429    0.7466   -1.0359 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6183    0.9585   -1.4290 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3335    1.0539   -1.7918 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0575    0.7851   -1.2789 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9138    0.2342   -0.0647 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3805   -0.0446    0.4691 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3278    0.9007    0.1879 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5490    0.3127    0.0379 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5265    0.8706    1.0470 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6402    2.2379    0.8395 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4075   -1.1662    0.3190 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2322   -1.9291   -0.5105 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9395   -1.3740   -0.0292 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8639   -1.4710   -1.4167 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0207   -0.0481    0.6354 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9030   -0.5645    1.7747 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0607   -0.1686    2.0866 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1940    0.6169    0.8865 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7663   -1.1398    0.6879 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4824    1.4937   -2.7589 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1941    1.0297   -1.8792 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3482   -0.1520    1.5934 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9722    0.4937   -0.9594 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5302    0.4239    0.8921 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1873    0.7300    2.0909 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1425    2.5373    0.0562 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6031   -1.3502    1.3847 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8585   -2.8221   -0.6296 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4955   -2.2311    0.4778 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6327   -1.0057   -1.8677 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  3  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 10 13  1  0
 13 14  1  0
 13 15  1  0
 15 16  1  0
  7 17  1  0
 17 18  2  0
 17  2  1  0
 15  8  1  0
  1 19  1  0
  1 20  1  0
  1 21  1  0
  5 22  1  0
  6 23  1  0
  8 24  1  0
 10 25  1  0
 11 26  1  0
 11 27  1  0
 12 28  1  0
 13 29  1  0
 14 30  1  0
 15 31  1  0
 16 32  1  0
M  END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
3-Methyl-uridine	HMDB
N-3-Methyluridine	HMDB
N3-Methyluridine	HMDB
3-Methyluridine	MeSH

Chemical Formula

C₁₀H₁₄N₂O₆

Average Molecular Weight

258.228

Monoisotopic Molecular Weight

258.08518619

IUPAC Name

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

Traditional Name

N-3-methyluridine

CAS Registry Number

2140-69-4

SMILES

CN1C(=O)C=CN(C2OC(CO)C(O)C2O)C1=O

InChI Identifier

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

InChI Key

UTQUILVPBZEHTK-UHFFFAOYSA-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

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (HMDB: HMDB0004813)

Excreta

Biofluid or Excreta

Urine (PMID: 15116424)

Source

Endogenous

Endogenous (HMDB: HMDB0004813)

Pheasant (FooDB: FOOD00430)
Squab (FooDB: FOOD00481)
Turkey (FooDB: FOOD00494)
Quail (FooDB: FOOD00541)
Anatidae (FooDB: FOOD00576)
Rock ptarmigan (FooDB: FOOD00597)
Columbidae (Dove, Pigeon) (FooDB: FOOD00610)
Chicken (FooDB: FOOD00329)
Mallard duck (FooDB: FOOD00353)
Emu (FooDB: FOOD00360)
Greylag goose (FooDB: FOOD00368)
Guinea hen (FooDB: FOOD00373)
Ostrich (FooDB: FOOD00422)
Velvet duck (FooDB: FOOD00427)

Lagomorph

Ovis

Sheep (Mutton, Lamb) (FooDB: FOOD00473)

Bovine

Venison

Deer (FooDB: FOOD00524)
Mule deer (FooDB: FOOD00348)
Elk (FooDB: FOOD00359)

Caprae

Domestic goat (FooDB: FOOD00529)

Swine

Domestic pig (FooDB: FOOD00536)
Wild boar (FooDB: FOOD00307)

Equine

Horse (FooDB: FOOD00378)

Process

Not Available

Role

Not Available

Physical Properties

State

Solid

Experimental Molecular Properties

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

Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct Type	Data Source	CCS Value (Å²)	Reference
[M-H]-	MetCCS_train_neg	166.839	30932474

Predicted Molecular Properties

Property	Value	Source
Water Solubility	257 g/L	ALOGPS
logP	-1.4	ALOGPS
logP	-2.2	ChemAxon
logS	0	ALOGPS
pKa (Strongest Acidic)	12.55	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	110.54 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	57.46 m³·mol⁻¹	ChemAxon
Polarizability	24.21 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	158.813	31661259
DarkChem	[M-H]-	156.736	31661259
DeepCCS	[M+H]+	155.648	30932474
DeepCCS	[M-H]-	153.29	30932474
DeepCCS	[M-2H]-	187.01	30932474
DeepCCS	[M+Na]+	161.927	30932474
AllCCS	[M+H]+	158.1	32859911
AllCCS	[M+H-H2O]+	154.4	32859911
AllCCS	[M+NH4]+	161.5	32859911
AllCCS	[M+Na]+	162.5	32859911
AllCCS	[M-H]-	156.5	32859911
AllCCS	[M+Na-2H]-	156.5	32859911
AllCCS	[M+HCOO]-	156.6	32859911

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.	2.04 minutes	32390414
Predicted by Siyang on May 30, 2022	8.9376 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	3.53 minutes	32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid	156.1 seconds	40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	557.1 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	229.1 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	74.0 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	153.6 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	43.8 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	272.1 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	247.9 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	351.1 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	563.1 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	139.2 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	859.1 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	169.1 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	186.3 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	516.1 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	328.4 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	227.7 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
3-Methyluridine	CN1C(=O)C=CN(C2OC(CO)C(O)C2O)C1=O	3199.5	Standard polar	33892256
3-Methyluridine	CN1C(=O)C=CN(C2OC(CO)C(O)C2O)C1=O	1885.5	Standard non polar	33892256
3-Methyluridine	CN1C(=O)C=CN(C2OC(CO)C(O)C2O)C1=O	2323.4	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
3-Methyluridine,1TMS,isomer #1	CN1C(=O)C=CN(C2OC(CO[Si](C)(C)C)C(O)C2O)C1=O	2466.9	Semi standard non polar	33892256
3-Methyluridine,1TMS,isomer #2	CN1C(=O)C=CN(C2OC(CO)C(O[Si](C)(C)C)C2O)C1=O	2501.0	Semi standard non polar	33892256
3-Methyluridine,1TMS,isomer #3	CN1C(=O)C=CN(C2OC(CO)C(O)C2O[Si](C)(C)C)C1=O	2490.1	Semi standard non polar	33892256
3-Methyluridine,2TMS,isomer #1	CN1C(=O)C=CN(C2OC(CO[Si](C)(C)C)C(O[Si](C)(C)C)C2O)C1=O	2497.5	Semi standard non polar	33892256
3-Methyluridine,2TMS,isomer #2	CN1C(=O)C=CN(C2OC(CO[Si](C)(C)C)C(O)C2O[Si](C)(C)C)C1=O	2501.2	Semi standard non polar	33892256
3-Methyluridine,2TMS,isomer #3	CN1C(=O)C=CN(C2OC(CO)C(O[Si](C)(C)C)C2O[Si](C)(C)C)C1=O	2485.0	Semi standard non polar	33892256
3-Methyluridine,3TMS,isomer #1	CN1C(=O)C=CN(C2OC(CO[Si](C)(C)C)C(O[Si](C)(C)C)C2O[Si](C)(C)C)C1=O	2466.3	Semi standard non polar	33892256
3-Methyluridine,1TBDMS,isomer #1	CN1C(=O)C=CN(C2OC(CO[Si](C)(C)C(C)(C)C)C(O)C2O)C1=O	2772.1	Semi standard non polar	33892256
3-Methyluridine,1TBDMS,isomer #2	CN1C(=O)C=CN(C2OC(CO)C(O[Si](C)(C)C(C)(C)C)C2O)C1=O	2767.0	Semi standard non polar	33892256
3-Methyluridine,1TBDMS,isomer #3	CN1C(=O)C=CN(C2OC(CO)C(O)C2O[Si](C)(C)C(C)(C)C)C1=O	2766.0	Semi standard non polar	33892256
3-Methyluridine,2TBDMS,isomer #1	CN1C(=O)C=CN(C2OC(CO[Si](C)(C)C(C)(C)C)C(O[Si](C)(C)C(C)(C)C)C2O)C1=O	3000.0	Semi standard non polar	33892256
3-Methyluridine,2TBDMS,isomer #2	CN1C(=O)C=CN(C2OC(CO[Si](C)(C)C(C)(C)C)C(O)C2O[Si](C)(C)C(C)(C)C)C1=O	2991.6	Semi standard non polar	33892256
3-Methyluridine,2TBDMS,isomer #3	CN1C(=O)C=CN(C2OC(CO)C(O[Si](C)(C)C(C)(C)C)C2O[Si](C)(C)C(C)(C)C)C1=O	2969.0	Semi standard non polar	33892256
3-Methyluridine,3TBDMS,isomer #1	CN1C(=O)C=CN(C2OC(CO[Si](C)(C)C(C)(C)C)C(O[Si](C)(C)C(C)(C)C)C2O[Si](C)(C)C(C)(C)C)C1=O	3196.6	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - 3-Methyluridine GC-MS (Non-derivatized) - 70eV, Positive	splash10-05i3-9420000000-6bfd41e6dad3d99bdefd	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3-Methyluridine GC-MS (3 TMS) - 70eV, Positive	splash10-0avr-7869500000-8ecdc253935419deafbb	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3-Methyluridine GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3-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
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Methyluridine 10V, Positive-QTOF	splash10-004i-0920000000-390bf2ef89850c7a98fb	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Methyluridine 20V, Positive-QTOF	splash10-004i-6900000000-b3415da0734ebf4dd298	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Methyluridine 40V, Positive-QTOF	splash10-00os-9400000000-12ca095eec130dc54ea9	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Methyluridine 10V, Negative-QTOF	splash10-0a4i-6790000000-d0867dbab6597fc7bb3f	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Methyluridine 20V, Negative-QTOF	splash10-0a6r-8930000000-0566e352d9e609c17494	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Methyluridine 40V, Negative-QTOF	splash10-0006-9100000000-7a60aac30d942df68cb4	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Methyluridine 10V, Negative-QTOF	splash10-00or-2900000000-4fc534f0dece37218939	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Methyluridine 20V, Negative-QTOF	splash10-02dr-4900000000-cf65f9e10d55af99c984	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Methyluridine 40V, Negative-QTOF	splash10-014m-9100000000-4e419ba43aeba839b027	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Methyluridine 10V, Positive-QTOF	splash10-004i-2900000000-68e7cf8708827caffc0a	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Methyluridine 20V, Positive-QTOF	splash10-004i-5900000000-a4a25fd5fc204c9e85a4	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Methyluridine 40V, Positive-QTOF	splash10-004i-7900000000-e0953d880cd7c41bd4e8	2021-09-25	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood
Urine

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Expected but not Quantified	Not Quantified	Not Available	Not Available	Normal	Not Available	details
Urine	Detected and Quantified	0.39 (0.33-0.44) umol/mmol creatinine	Adult (>18 years old)	Both	Normal	15116424	details
Urine	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Female	Normal	19010317	details

Abnormal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Urine	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Female	Ovarian cancer	19010317	details

Associated Disorders and Diseases

Disease References

Ovarian cancer
Woo HM, Kim KM, Choi MH, Jung BH, Lee J, Kong G, Nam SJ, Kim S, Bai SW, Chung BC: Mass spectrometry based metabolomic approaches in urinary biomarker study of women's cancers. Clin Chim Acta. 2009 Feb;400(1-2):63-9. doi: 10.1016/j.cca.2008.10.014. Epub 2008 Oct 30. [PubMed:19010317 ]

Associated OMIM IDs

167000 (Ovarian cancer)

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB023424

KNApSAcK ID

Not Available

Chemspider ID

280553

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

5-Methyluridine

METLIN ID

7077

PubChem Compound

316991

PDB ID

Not Available

ChEBI ID

89487

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Levene, P. A.; Tipson, R. Stuart. N-Methyluridine and its bearing on the structure of uridine. Journal of Biological Chemistry (1934), 104 385-93.

Material Safety Data Sheet (MSDS)

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. [PubMed:15116424 ]
Kammerer B, Frickenschmidt A, Muller CE, Laufer S, Gleiter CH, Liebich H: Mass spectrometric identification of modified urinary nucleosides used as potential biomedical markers by LC-ITMS coupling. Anal Bioanal Chem. 2005 Jun;382(4):1017-26. Epub 2005 May 19. [PubMed:15906010 ]

Showing metabocard for 3-Methyluridine (HMDB0004813)

MOL for HMDB0004813 (3-Methyluridine)

3D MOL for HMDB0004813 (3-Methyluridine)

3D SDF for HMDB0004813 (3-Methyluridine)

3D-SDF for HMDB0004813 (3-Methyluridine)

PDB for HMDB0004813 (3-Methyluridine)

3D PDB for HMDB0004813 (3-Methyluridine)

SMILES for HMDB0004813 (3-Methyluridine)

INCHI for HMDB0004813 (3-Methyluridine)

Structure for HMDB0004813 (3-Methyluridine)

3D Structure for HMDB0004813 (3-Methyluridine)

Experimental Collision Cross Sections

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra