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Record Information

Version

5.0

Status

Detected and Quantified

Creation Date

2005-11-16 15:48:42 UTC

Update Date

2021-09-14 15:44:40 UTC

HMDB ID

HMDB0000788

Secondary Accession Numbers

HMDB00788

Metabolite Identification

Common Name

Orotidine

Description

Orotidine is a nucleoside formed by attaching orotic acid to a ribose ring via a beta-N1-glycosidic bond. It is a water-soluble solid. Orotidine is found in bacteria, fungi, plants, and animals. In humans, orotidine occurs as its 5'-phosphate (orotidylic acid), which is an intermediate in the biosynthesis of pyrimidine nucleosides (cytidine and uridine) that are found in nucleic acids (as the nucleotides containing the bases cytosine and uracil). Orotidine itself is not a component of nucleic acid. Orotidine monophosphate (OMP) is converted to uridine monophosphate by OMP decarboxylase, which is inhibited by mononucleotide precursors. Large amounts of orotidine are excreted in the urine of cancer patients treated with 6-azauridine, which is one such inhibitor, indicating that the subject has increased DNA synthesis due to cancer. Orotidine was first isolated from a mutant strain of the fungus Neurospora by A. Michael Michelson, William Drell, and Herschel K. Mitchell (PMID: 14853953 ).

Structure

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

HMDB0000788
     RDKit          3D
Orotidine
 32 33  0  0  0  0  0  0  0  0999 V2000
    3.1468    0.4429    2.5898 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1095    0.2711    1.8555 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9784    0.1448    2.5491 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2825    0.2405    0.4493 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6008    0.4487   -0.0400 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8631    0.4556   -1.3746 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0161    0.6371   -1.8104 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8493    0.2621   -2.2024 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6266    0.0689   -1.7253 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7342   -0.1047   -2.6318 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2600    0.0431   -0.3882 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0804   -0.1962   -0.1742 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.9608    0.9143   -0.3303 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2139    0.3139   -0.4717 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.2356    1.0622    0.3907 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3217    2.3988   -0.0075 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1246   -1.1009    0.0834 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.8344   -2.0477   -0.8667 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7616   -0.9139    0.8832 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.4022   -2.2020    1.1594 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6524    0.8059    3.2304 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4048    0.6039    0.6718 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0359    0.2648   -3.2602 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4186   -0.8122   -1.1314 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4998    0.3409   -1.5288 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9240    0.9849    1.4482 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2402    0.6243    0.2831 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0367    2.5076   -0.9483 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9202   -1.3668    0.7721 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6847   -2.3301   -1.2828 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2051   -0.3383    1.7340 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6957   -2.4231    2.0750 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  2  0
  6  8  1  0
  8  9  1  0
  9 10  2  0
  9 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 14 17  1  0
 17 18  1  0
 17 19  1  0
 19 20  1  0
 11  4  1  0
 19 12  1  0
  3 21  1  0
  5 22  1  0
  8 23  1  0
 12 24  1  6
 14 25  1  6
 15 26  1  0
 15 27  1  0
 16 28  1  0
 17 29  1  1
 18 30  1  0
 19 31  1  1
 20 32  1  0
M  END


  Mrv1652305271900242D          

 20 21  0  0  1  0            999 V2000
   22.0177  -14.2859    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   24.1372  -14.0308    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   23.5826  -15.7379    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   20.9672  -15.6516    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   24.1141  -12.9759    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   20.5417  -12.5634    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   22.6851  -10.5009    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   21.2562  -13.8009    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   22.6851  -12.9759    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   23.3996  -11.7384    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   23.3526  -14.2859    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   23.0976  -15.0704    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   22.6851  -13.8009    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   22.2726  -15.0704    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   21.7877  -15.7379    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   21.9707  -12.5634    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.3996  -12.5634    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   21.9707  -11.7384    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   22.6851  -11.3259    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   21.2562  -12.9759    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1 13  1  0  0  0  0
  1 14  1  0  0  0  0
 11  2  1  6  0  0  0
 12  3  1  6  0  0  0
  4 15  1  0  0  0  0
  5 17  2  0  0  0  0
  6 20  1  0  0  0  0
  7 19  2  0  0  0  0
  8 20  2  0  0  0  0
 13  9  1  1  0  0  0
  9 16  1  0  0  0  0
  9 17  1  0  0  0  0
 10 17  1  0  0  0  0
 10 19  1  0  0  0  0
 11 12  1  0  0  0  0
 11 13  1  0  0  0  0
 12 14  1  0  0  0  0
 14 15  1  1  0  0  0
 16 18  2  0  0  0  0
 16 20  1  0  0  0  0
 18 19  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0000788

> <DATABASE_NAME>
hmdb

> <SMILES>
OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C(=O)NC(=O)C=C1C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C10H12N2O8/c13-2-4-6(15)7(16)8(20-4)12-3(9(17)18)1-5(14)11-10(12)19/h1,4,6-8,13,15-16H,2H2,(H,17,18)(H,11,14,19)/t4-,6-,7-,8-/m1/s1

> <INCHI_KEY>
FKCRAVPPBFWEJD-XVFCMESISA-N

> <FORMULA>
C10H12N2O8

> <MOLECULAR_WEIGHT>
288.2109

> <EXACT_MASS>
288.05936537

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
32

> <JCHEM_AVERAGE_POLARIZABILITY>
25.003434122411154

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid

> <ALOGPS_LOGP>
-2.04

> <JCHEM_LOGP>
-2.7876156426666667

> <ALOGPS_LOGS>
-0.81

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
9.682367621598052

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.8566931418927357

> <JCHEM_PKA_STRONGEST_BASIC>
-2.980299871615192

> <JCHEM_POLAR_SURFACE_AREA>
156.63000000000002

> <JCHEM_REFRACTIVITY>
59.870900000000006

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.47e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
orotidine

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0000788
     RDKit          3D
Orotidine
 32 33  0  0  0  0  0  0  0  0999 V2000
    3.1468    0.4429    2.5898 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1095    0.2711    1.8555 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9784    0.1448    2.5491 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2825    0.2405    0.4493 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6008    0.4487   -0.0400 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8631    0.4556   -1.3746 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0161    0.6371   -1.8104 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8493    0.2621   -2.2024 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6266    0.0689   -1.7253 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7342   -0.1047   -2.6318 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2600    0.0431   -0.3882 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0804   -0.1962   -0.1742 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.9608    0.9143   -0.3303 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2139    0.3139   -0.4717 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.2356    1.0622    0.3907 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3217    2.3988   -0.0075 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1246   -1.1009    0.0834 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.8344   -2.0477   -0.8667 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7616   -0.9139    0.8832 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.4022   -2.2020    1.1594 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6524    0.8059    3.2304 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4048    0.6039    0.6718 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0359    0.2648   -3.2602 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4186   -0.8122   -1.1314 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4998    0.3409   -1.5288 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9240    0.9849    1.4482 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2402    0.6243    0.2831 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0367    2.5076   -0.9483 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9202   -1.3668    0.7721 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6847   -2.3301   -1.2828 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2051   -0.3383    1.7340 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6957   -2.4231    2.0750 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  2  0
  6  8  1  0
  8  9  1  0
  9 10  2  0
  9 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 14 17  1  0
 17 18  1  0
 17 19  1  0
 19 20  1  0
 11  4  1  0
 19 12  1  0
  3 21  1  0
  5 22  1  0
  8 23  1  0
 12 24  1  6
 14 25  1  6
 15 26  1  0
 15 27  1  0
 16 28  1  0
 17 29  1  1
 18 30  1  0
 19 31  1  1
 20 32  1  0
M  END

HEADER    PROTEIN                                 27-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-MAY-19         0                                  
HETATM    1  O   UNK     0      41.100 -26.667   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      45.056 -26.191   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      44.021 -29.377   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      39.139 -29.216   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0      45.013 -24.222   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0      38.345 -23.452   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0      42.346 -19.602   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      39.678 -25.762   0.000  0.00  0.00           O+0
HETATM    9  N   UNK     0      42.346 -24.222   0.000  0.00  0.00           N+0
HETATM   10  N   UNK     0      43.679 -21.912   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0      43.592 -26.667   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      43.116 -28.131   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      42.346 -25.762   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      41.576 -28.131   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      40.670 -29.377   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      41.012 -23.452   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      43.679 -23.452   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      41.012 -21.912   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      42.346 -21.142   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      39.678 -24.222   0.000  0.00  0.00           C+0
CONECT    1   13   14                                                       
CONECT    2   11                                                            
CONECT    3   12                                                            
CONECT    4   15                                                            
CONECT    5   17                                                            
CONECT    6   20                                                            
CONECT    7   19                                                            
CONECT    8   20                                                            
CONECT    9   13   16   17                                                  
CONECT   10   17   19                                                       
CONECT   11    2   12   13                                                  
CONECT   12    3   11   14                                                  
CONECT   13    1    9   11                                                  
CONECT   14    1   12   15                                                  
CONECT   15    4   14                                                       
CONECT   16    9   18   20                                                  
CONECT   17    5    9   10                                                  
CONECT   18   16   19                                                       
CONECT   19    7   10   18                                                  
CONECT   20    6    8   16                                                  
MASTER        0    0    0    0    0    0    0    0   20    0   42    0
END

COMPND    HMDB0000788
HETATM    1  O1  UNL     1       3.147   0.443   2.590  1.00  0.00           O  
HETATM    2  C1  UNL     1       2.109   0.271   1.855  1.00  0.00           C  
HETATM    3  O2  UNL     1       0.978   0.145   2.549  1.00  0.00           O  
HETATM    4  C2  UNL     1       2.283   0.240   0.449  1.00  0.00           C  
HETATM    5  C3  UNL     1       3.601   0.449  -0.040  1.00  0.00           C  
HETATM    6  C4  UNL     1       3.863   0.456  -1.375  1.00  0.00           C  
HETATM    7  O3  UNL     1       5.016   0.637  -1.810  1.00  0.00           O  
HETATM    8  N1  UNL     1       2.849   0.262  -2.202  1.00  0.00           N  
HETATM    9  C5  UNL     1       1.627   0.069  -1.725  1.00  0.00           C  
HETATM   10  O4  UNL     1       0.734  -0.105  -2.632  1.00  0.00           O  
HETATM   11  N2  UNL     1       1.260   0.043  -0.388  1.00  0.00           N  
HETATM   12  C6  UNL     1      -0.080  -0.196  -0.174  1.00  0.00           C  
HETATM   13  O5  UNL     1      -0.961   0.914  -0.330  1.00  0.00           O  
HETATM   14  C7  UNL     1      -2.214   0.314  -0.472  1.00  0.00           C  
HETATM   15  C8  UNL     1      -3.236   1.062   0.391  1.00  0.00           C  
HETATM   16  O6  UNL     1      -3.322   2.399  -0.008  1.00  0.00           O  
HETATM   17  C9  UNL     1      -2.125  -1.101   0.083  1.00  0.00           C  
HETATM   18  O7  UNL     1      -1.834  -2.048  -0.867  1.00  0.00           O  
HETATM   19  C10 UNL     1      -0.762  -0.914   0.883  1.00  0.00           C  
HETATM   20  O8  UNL     1      -0.402  -2.202   1.159  1.00  0.00           O  
HETATM   21  H1  UNL     1       0.652   0.806   3.230  1.00  0.00           H  
HETATM   22  H2  UNL     1       4.405   0.604   0.672  1.00  0.00           H  
HETATM   23  H3  UNL     1       3.036   0.265  -3.260  1.00  0.00           H  
HETATM   24  H4  UNL     1      -0.419  -0.812  -1.131  1.00  0.00           H  
HETATM   25  H5  UNL     1      -2.500   0.341  -1.529  1.00  0.00           H  
HETATM   26  H6  UNL     1      -2.924   0.985   1.448  1.00  0.00           H  
HETATM   27  H7  UNL     1      -4.240   0.624   0.283  1.00  0.00           H  
HETATM   28  H8  UNL     1      -3.037   2.508  -0.948  1.00  0.00           H  
HETATM   29  H9  UNL     1      -2.920  -1.367   0.772  1.00  0.00           H  
HETATM   30  H10 UNL     1      -2.685  -2.330  -1.283  1.00  0.00           H  
HETATM   31  H11 UNL     1      -1.205  -0.338   1.734  1.00  0.00           H  
HETATM   32  H12 UNL     1      -0.696  -2.423   2.075  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3   21
CONECT    4    5    5   11
CONECT    5    6   22
CONECT    6    7    7    8
CONECT    8    9   23
CONECT    9   10   10   11
CONECT   11   12
CONECT   12   13   19   24
CONECT   13   14
CONECT   14   15   17   25
CONECT   15   16   26   27
CONECT   16   28
CONECT   17   18   19   29
CONECT   18   30
CONECT   19   20   31
CONECT   20   32
END

HMDB0000788
     RDKit          3D
Orotidine
 32 33  0  0  0  0  0  0  0  0999 V2000
    3.1468    0.4429    2.5898 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1095    0.2711    1.8555 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9784    0.1448    2.5491 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2825    0.2405    0.4493 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6008    0.4487   -0.0400 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8631    0.4556   -1.3746 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0161    0.6371   -1.8104 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8493    0.2621   -2.2024 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6266    0.0689   -1.7253 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7342   -0.1047   -2.6318 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2600    0.0431   -0.3882 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0804   -0.1962   -0.1742 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.9608    0.9143   -0.3303 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2139    0.3139   -0.4717 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.2356    1.0622    0.3907 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3217    2.3988   -0.0075 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1246   -1.1009    0.0834 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.8344   -2.0477   -0.8667 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7616   -0.9139    0.8832 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.4022   -2.2020    1.1594 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6524    0.8059    3.2304 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4048    0.6039    0.6718 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0359    0.2648   -3.2602 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4186   -0.8122   -1.1314 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4998    0.3409   -1.5288 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9240    0.9849    1.4482 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2402    0.6243    0.2831 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0367    2.5076   -0.9483 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9202   -1.3668    0.7721 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6847   -2.3301   -1.2828 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2051   -0.3383    1.7340 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6957   -2.4231    2.0750 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  2  0
  6  8  1  0
  8  9  1  0
  9 10  2  0
  9 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 14 17  1  0
 17 18  1  0
 17 19  1  0
 19 20  1  0
 11  4  1  0
 19 12  1  0
  3 21  1  0
  5 22  1  0
  8 23  1  0
 12 24  1  6
 14 25  1  6
 15 26  1  0
 15 27  1  0
 16 28  1  0
 17 29  1  1
 18 30  1  0
 19 31  1  1
 20 32  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
3-Ribofuranosylorotic acid	ChEBI
6-Carboxyuridine	ChEBI
3-Ribofuranosylorotate	Generator
Orotic acid riboside	HMDB
Orotidine, ammonium salt	HMDB

Chemical Formula

C₁₀H₁₂N₂O₈

Average Molecular Weight

288.2109

Monoisotopic Molecular Weight

288.05936537

IUPAC Name

3-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid

Traditional Name

orotidine

CAS Registry Number

314-50-1

SMILES

OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C(=O)NC(=O)C=C1C(O)=O

InChI Identifier

InChI=1S/C10H12N2O8/c13-2-4-6(15)7(16)8(20-4)12-3(9(17)18)1-5(14)11-10(12)19/h1,4,6-8,13,15-16H,2H2,(H,17,18)(H,11,14,19)/t4-,6-,7-,8-/m1/s1

InChI Key

FKCRAVPPBFWEJD-XVFCMESISA-N

Chemical Taxonomy

Description

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

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Pyrimidine nucleosides

Sub Class

Not Available

Direct Parent

Pyrimidine nucleosides

Alternative Parents

Substituents

Pyrimidine nucleoside
Glycosyl compound
N-glycosyl compound
Pentose monosaccharide
Hydropyrimidine carboxylic acid derivative
Pyrimidine-6-carboxylic acid
Pyrimidine-6-carboxylic acid or derivatives
Hydroxypyrimidine
Pyrimidone
Hydropyrimidine
Monosaccharide
Pyrimidine
Heteroaromatic compound
Tetrahydrofuran
Secondary alcohol
Azacycle
Carboxylic acid derivative
Oxacycle
Organoheterocyclic compound
Carboxylic acid
Monocarboxylic acid or derivatives
Hydrocarbon derivative
Organonitrogen compound
Alcohol
Organopnictogen compound
Organic oxygen compound
Organic nitrogen compound
Organooxygen compound
Organic oxide
Primary alcohol
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

uridines (CHEBI:25722 )
pyrimidinemonocarboxylic acid (CHEBI:25722 )
nucleoside (CHEBI:25722 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 7877593)

Organ

Placenta (HMDB: HMDB0000788)

Excreta

Biofluid or Excreta

Urine (PMID: 25757096)

Cellular substructure

Cytoplasm (HMDB: HMDB0000788)

Source

Endogenous

Endogenous (HMDB: HMDB0000788)

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)

Pulse

Bean

Yellow wax bean (FooDB: FOOD00882)
Green bean (FooDB: FOOD00883)

Pulses (FooDB: FOOD00867)

Process

Not Available

Role

Industrial application

Pharmaceutical industry

Biomarker

Orotic Aciduria (MarkerDB: MDB00000252)

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	> 400 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	44.7 g/L	ALOGPS
logP	-2	ALOGPS
logP	-2.8	ChemAxon
logS	-0.81	ALOGPS
pKa (Strongest Acidic)	2.86	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	156.63 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	59.87 m³·mol⁻¹	ChemAxon
Polarizability	25 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]+	163.455	31661259
DarkChem	[M-H]-	159.937	31661259
AllCCS	[M+H]+	162.465	32859911
AllCCS	[M-H]-	159.26	32859911
DeepCCS	[M+H]+	162.99	30932474
DeepCCS	[M-H]-	160.595	30932474
DeepCCS	[M-2H]-	194.632	30932474
DeepCCS	[M+Na]+	169.627	30932474
AllCCS	[M+H]+	162.5	32859911
AllCCS	[M+H-H2O]+	159.0	32859911
AllCCS	[M+NH4]+	165.6	32859911
AllCCS	[M+Na]+	166.6	32859911
AllCCS	[M-H]-	159.3	32859911
AllCCS	[M+Na-2H]-	159.0	32859911
AllCCS	[M+HCOO]-	158.8	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.	2.17 minutes	32390414
Predicted by Siyang on May 30, 2022	9.8938 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	7.94 minutes	32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid	276.2 seconds	40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	542.2 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	254.2 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	48.7 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	157.5 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	52.4 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	295.7 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	248.8 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	661.7 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	578.4 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	68.6 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	927.9 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	173.4 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	198.1 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	595.6 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	338.1 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	375.1 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Orotidine	OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C(=O)NC(=O)C=C1C(O)=O	3713.4	Standard polar	33892256
Orotidine	OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C(=O)NC(=O)C=C1C(O)=O	2247.4	Standard non polar	33892256
Orotidine	OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C(=O)NC(=O)C=C1C(O)=O	2863.4	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Orotidine,1TMS,isomer #1	C[Si](C)(C)OC[C@H]1O[C@@H](N2C(C(=O)O)=CC(=O)[NH]C2=O)[C@H](O)[C@@H]1O	2558.8	Semi standard non polar	33892256
Orotidine,1TMS,isomer #2	C[Si](C)(C)O[C@@H]1[C@H](O)[C@@H](CO)O[C@H]1N1C(C(=O)O)=CC(=O)[NH]C1=O	2576.5	Semi standard non polar	33892256
Orotidine,1TMS,isomer #3	C[Si](C)(C)O[C@@H]1[C@@H](CO)O[C@@H](N2C(C(=O)O)=CC(=O)[NH]C2=O)[C@@H]1O	2583.9	Semi standard non polar	33892256
Orotidine,1TMS,isomer #4	C[Si](C)(C)OC(=O)C1=CC(=O)[NH]C(=O)N1[C@@H]1O[C@H](CO)[C@@H](O)[C@H]1O	2556.0	Semi standard non polar	33892256
Orotidine,1TMS,isomer #5	C[Si](C)(C)N1C(=O)C=C(C(=O)O)N([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)C1=O	2615.9	Semi standard non polar	33892256
Orotidine,2TMS,isomer #1	C[Si](C)(C)OC[C@H]1O[C@@H](N2C(C(=O)O[Si](C)(C)C)=CC(=O)[NH]C2=O)[C@H](O)[C@@H]1O	2532.3	Semi standard non polar	33892256
Orotidine,2TMS,isomer #10	C[Si](C)(C)OC(=O)C1=CC(=O)N([Si](C)(C)C)C(=O)N1[C@@H]1O[C@H](CO)[C@@H](O)[C@H]1O	2604.7	Semi standard non polar	33892256
Orotidine,2TMS,isomer #2	C[Si](C)(C)OC[C@H]1O[C@@H](N2C(C(=O)O)=CC(=O)[NH]C2=O)[C@H](O[Si](C)(C)C)[C@@H]1O	2558.3	Semi standard non polar	33892256
Orotidine,2TMS,isomer #3	C[Si](C)(C)OC[C@H]1O[C@@H](N2C(C(=O)O)=CC(=O)[NH]C2=O)[C@H](O)[C@@H]1O[Si](C)(C)C	2559.1	Semi standard non polar	33892256
Orotidine,2TMS,isomer #4	C[Si](C)(C)OC[C@H]1O[C@@H](N2C(C(=O)O)=CC(=O)N([Si](C)(C)C)C2=O)[C@H](O)[C@@H]1O	2594.1	Semi standard non polar	33892256
Orotidine,2TMS,isomer #5	C[Si](C)(C)O[C@@H]1[C@@H](CO)O[C@@H](N2C(C(=O)O)=CC(=O)[NH]C2=O)[C@@H]1O[Si](C)(C)C	2577.5	Semi standard non polar	33892256
Orotidine,2TMS,isomer #6	C[Si](C)(C)OC(=O)C1=CC(=O)[NH]C(=O)N1[C@@H]1O[C@H](CO)[C@@H](O)[C@H]1O[Si](C)(C)C	2545.9	Semi standard non polar	33892256
Orotidine,2TMS,isomer #7	C[Si](C)(C)O[C@@H]1[C@H](O)[C@@H](CO)O[C@H]1N1C(C(=O)O)=CC(=O)N([Si](C)(C)C)C1=O	2608.9	Semi standard non polar	33892256
Orotidine,2TMS,isomer #8	C[Si](C)(C)OC(=O)C1=CC(=O)[NH]C(=O)N1[C@@H]1O[C@H](CO)[C@@H](O[Si](C)(C)C)[C@H]1O	2577.8	Semi standard non polar	33892256
Orotidine,2TMS,isomer #9	C[Si](C)(C)O[C@@H]1[C@@H](CO)O[C@@H](N2C(C(=O)O)=CC(=O)N([Si](C)(C)C)C2=O)[C@@H]1O	2613.8	Semi standard non polar	33892256
Orotidine,3TMS,isomer #1	C[Si](C)(C)OC[C@H]1O[C@@H](N2C(C(=O)O[Si](C)(C)C)=CC(=O)[NH]C2=O)[C@H](O[Si](C)(C)C)[C@@H]1O	2528.6	Semi standard non polar	33892256
Orotidine,3TMS,isomer #10	C[Si](C)(C)OC(=O)C1=CC(=O)N([Si](C)(C)C)C(=O)N1[C@@H]1O[C@H](CO)[C@@H](O[Si](C)(C)C)[C@H]1O	2618.5	Semi standard non polar	33892256
Orotidine,3TMS,isomer #2	C[Si](C)(C)OC[C@H]1O[C@@H](N2C(C(=O)O[Si](C)(C)C)=CC(=O)[NH]C2=O)[C@H](O)[C@@H]1O[Si](C)(C)C	2532.8	Semi standard non polar	33892256
Orotidine,3TMS,isomer #3	C[Si](C)(C)OC[C@H]1O[C@@H](N2C(C(=O)O[Si](C)(C)C)=CC(=O)N([Si](C)(C)C)C2=O)[C@H](O)[C@@H]1O	2582.0	Semi standard non polar	33892256
Orotidine,3TMS,isomer #4	C[Si](C)(C)OC[C@H]1O[C@@H](N2C(C(=O)O)=CC(=O)[NH]C2=O)[C@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C	2531.1	Semi standard non polar	33892256
Orotidine,3TMS,isomer #5	C[Si](C)(C)OC[C@H]1O[C@@H](N2C(C(=O)O)=CC(=O)N([Si](C)(C)C)C2=O)[C@H](O[Si](C)(C)C)[C@@H]1O	2587.5	Semi standard non polar	33892256
Orotidine,3TMS,isomer #6	C[Si](C)(C)OC[C@H]1O[C@@H](N2C(C(=O)O)=CC(=O)N([Si](C)(C)C)C2=O)[C@H](O)[C@@H]1O[Si](C)(C)C	2593.4	Semi standard non polar	33892256
Orotidine,3TMS,isomer #7	C[Si](C)(C)OC(=O)C1=CC(=O)[NH]C(=O)N1[C@@H]1O[C@H](CO)[C@@H](O[Si](C)(C)C)[C@H]1O[Si](C)(C)C	2528.9	Semi standard non polar	33892256
Orotidine,3TMS,isomer #8	C[Si](C)(C)O[C@@H]1[C@@H](CO)O[C@@H](N2C(C(=O)O)=CC(=O)N([Si](C)(C)C)C2=O)[C@@H]1O[Si](C)(C)C	2610.0	Semi standard non polar	33892256
Orotidine,3TMS,isomer #9	C[Si](C)(C)OC(=O)C1=CC(=O)N([Si](C)(C)C)C(=O)N1[C@@H]1O[C@H](CO)[C@@H](O)[C@H]1O[Si](C)(C)C	2604.0	Semi standard non polar	33892256
Orotidine,4TMS,isomer #1	C[Si](C)(C)OC[C@H]1O[C@@H](N2C(C(=O)O[Si](C)(C)C)=CC(=O)[NH]C2=O)[C@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C	2527.4	Semi standard non polar	33892256
Orotidine,4TMS,isomer #2	C[Si](C)(C)OC[C@H]1O[C@@H](N2C(C(=O)O[Si](C)(C)C)=CC(=O)N([Si](C)(C)C)C2=O)[C@H](O[Si](C)(C)C)[C@@H]1O	2610.8	Semi standard non polar	33892256
Orotidine,4TMS,isomer #3	C[Si](C)(C)OC[C@H]1O[C@@H](N2C(C(=O)O[Si](C)(C)C)=CC(=O)N([Si](C)(C)C)C2=O)[C@H](O)[C@@H]1O[Si](C)(C)C	2614.8	Semi standard non polar	33892256
Orotidine,4TMS,isomer #4	C[Si](C)(C)OC[C@H]1O[C@@H](N2C(C(=O)O)=CC(=O)N([Si](C)(C)C)C2=O)[C@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C	2600.8	Semi standard non polar	33892256
Orotidine,4TMS,isomer #5	C[Si](C)(C)OC(=O)C1=CC(=O)N([Si](C)(C)C)C(=O)N1[C@@H]1O[C@H](CO)[C@@H](O[Si](C)(C)C)[C@H]1O[Si](C)(C)C	2622.6	Semi standard non polar	33892256
Orotidine,5TMS,isomer #1	C[Si](C)(C)OC[C@H]1O[C@@H](N2C(C(=O)O[Si](C)(C)C)=CC(=O)N([Si](C)(C)C)C2=O)[C@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C	2620.8	Semi standard non polar	33892256
Orotidine,5TMS,isomer #1	C[Si](C)(C)OC[C@H]1O[C@@H](N2C(C(=O)O[Si](C)(C)C)=CC(=O)N([Si](C)(C)C)C2=O)[C@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C	2778.9	Standard non polar	33892256
Orotidine,5TMS,isomer #1	C[Si](C)(C)OC[C@H]1O[C@@H](N2C(C(=O)O[Si](C)(C)C)=CC(=O)N([Si](C)(C)C)C2=O)[C@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C	2801.1	Standard polar	33892256
Orotidine,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C(C(=O)O)=CC(=O)[NH]C2=O)[C@H](O)[C@@H]1O	2806.3	Semi standard non polar	33892256
Orotidine,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)O[C@@H]1[C@H](O)[C@@H](CO)O[C@H]1N1C(C(=O)O)=CC(=O)[NH]C1=O	2823.6	Semi standard non polar	33892256
Orotidine,1TBDMS,isomer #3	CC(C)(C)[Si](C)(C)O[C@@H]1[C@@H](CO)O[C@@H](N2C(C(=O)O)=CC(=O)[NH]C2=O)[C@@H]1O	2829.9	Semi standard non polar	33892256
Orotidine,1TBDMS,isomer #4	CC(C)(C)[Si](C)(C)OC(=O)C1=CC(=O)[NH]C(=O)N1[C@@H]1O[C@H](CO)[C@@H](O)[C@H]1O	2811.8	Semi standard non polar	33892256
Orotidine,1TBDMS,isomer #5	CC(C)(C)[Si](C)(C)N1C(=O)C=C(C(=O)O)N([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)C1=O	2853.7	Semi standard non polar	33892256
Orotidine,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C(C(=O)O[Si](C)(C)C(C)(C)C)=CC(=O)[NH]C2=O)[C@H](O)[C@@H]1O	3016.3	Semi standard non polar	33892256
Orotidine,2TBDMS,isomer #10	CC(C)(C)[Si](C)(C)OC(=O)C1=CC(=O)N([Si](C)(C)C(C)(C)C)C(=O)N1[C@@H]1O[C@H](CO)[C@@H](O)[C@H]1O	3079.0	Semi standard non polar	33892256
Orotidine,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C(C(=O)O)=CC(=O)[NH]C2=O)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O	3027.2	Semi standard non polar	33892256
Orotidine,2TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C(C(=O)O)=CC(=O)[NH]C2=O)[C@H](O)[C@@H]1O[Si](C)(C)C(C)(C)C	3012.5	Semi standard non polar	33892256
Orotidine,2TBDMS,isomer #4	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C(C(=O)O)=CC(=O)N([Si](C)(C)C(C)(C)C)C2=O)[C@H](O)[C@@H]1O	3067.9	Semi standard non polar	33892256
Orotidine,2TBDMS,isomer #5	CC(C)(C)[Si](C)(C)O[C@@H]1[C@@H](CO)O[C@@H](N2C(C(=O)O)=CC(=O)[NH]C2=O)[C@@H]1O[Si](C)(C)C(C)(C)C	3010.8	Semi standard non polar	33892256
Orotidine,2TBDMS,isomer #6	CC(C)(C)[Si](C)(C)OC(=O)C1=CC(=O)[NH]C(=O)N1[C@@H]1O[C@H](CO)[C@@H](O)[C@H]1O[Si](C)(C)C(C)(C)C	3014.9	Semi standard non polar	33892256
Orotidine,2TBDMS,isomer #7	CC(C)(C)[Si](C)(C)O[C@@H]1[C@H](O)[C@@H](CO)O[C@H]1N1C(C(=O)O)=CC(=O)N([Si](C)(C)C(C)(C)C)C1=O	3081.0	Semi standard non polar	33892256
Orotidine,2TBDMS,isomer #8	CC(C)(C)[Si](C)(C)OC(=O)C1=CC(=O)[NH]C(=O)N1[C@@H]1O[C@H](CO)[C@@H](O[Si](C)(C)C(C)(C)C)[C@H]1O	3019.4	Semi standard non polar	33892256
Orotidine,2TBDMS,isomer #9	CC(C)(C)[Si](C)(C)O[C@@H]1[C@@H](CO)O[C@@H](N2C(C(=O)O)=CC(=O)N([Si](C)(C)C(C)(C)C)C2=O)[C@@H]1O	3088.2	Semi standard non polar	33892256
Orotidine,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C(C(=O)O[Si](C)(C)C(C)(C)C)=CC(=O)[NH]C2=O)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O	3254.9	Semi standard non polar	33892256
Orotidine,3TBDMS,isomer #10	CC(C)(C)[Si](C)(C)OC(=O)C1=CC(=O)N([Si](C)(C)C(C)(C)C)C(=O)N1[C@@H]1O[C@H](CO)[C@@H](O[Si](C)(C)C(C)(C)C)[C@H]1O	3305.7	Semi standard non polar	33892256
Orotidine,3TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C(C(=O)O[Si](C)(C)C(C)(C)C)=CC(=O)[NH]C2=O)[C@H](O)[C@@H]1O[Si](C)(C)C(C)(C)C	3237.4	Semi standard non polar	33892256
Orotidine,3TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C(C(=O)O[Si](C)(C)C(C)(C)C)=CC(=O)N([Si](C)(C)C(C)(C)C)C2=O)[C@H](O)[C@@H]1O	3285.6	Semi standard non polar	33892256
Orotidine,3TBDMS,isomer #4	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C(C(=O)O)=CC(=O)[NH]C2=O)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O[Si](C)(C)C(C)(C)C	3193.5	Semi standard non polar	33892256
Orotidine,3TBDMS,isomer #5	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C(C(=O)O)=CC(=O)N([Si](C)(C)C(C)(C)C)C2=O)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O	3301.9	Semi standard non polar	33892256
Orotidine,3TBDMS,isomer #6	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C(C(=O)O)=CC(=O)N([Si](C)(C)C(C)(C)C)C2=O)[C@H](O)[C@@H]1O[Si](C)(C)C(C)(C)C	3297.0	Semi standard non polar	33892256
Orotidine,3TBDMS,isomer #7	CC(C)(C)[Si](C)(C)OC(=O)C1=CC(=O)[NH]C(=O)N1[C@@H]1O[C@H](CO)[C@@H](O[Si](C)(C)C(C)(C)C)[C@H]1O[Si](C)(C)C(C)(C)C	3217.3	Semi standard non polar	33892256
Orotidine,3TBDMS,isomer #8	CC(C)(C)[Si](C)(C)O[C@@H]1[C@@H](CO)O[C@@H](N2C(C(=O)O)=CC(=O)N([Si](C)(C)C(C)(C)C)C2=O)[C@@H]1O[Si](C)(C)C(C)(C)C	3307.3	Semi standard non polar	33892256
Orotidine,3TBDMS,isomer #9	CC(C)(C)[Si](C)(C)OC(=O)C1=CC(=O)N([Si](C)(C)C(C)(C)C)C(=O)N1[C@@H]1O[C@H](CO)[C@@H](O)[C@H]1O[Si](C)(C)C(C)(C)C	3299.5	Semi standard non polar	33892256
Orotidine,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C(C(=O)O[Si](C)(C)C(C)(C)C)=CC(=O)[NH]C2=O)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O[Si](C)(C)C(C)(C)C	3438.4	Semi standard non polar	33892256
Orotidine,4TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C(C(=O)O[Si](C)(C)C(C)(C)C)=CC(=O)N([Si](C)(C)C(C)(C)C)C2=O)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O	3514.1	Semi standard non polar	33892256
Orotidine,4TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C(C(=O)O[Si](C)(C)C(C)(C)C)=CC(=O)N([Si](C)(C)C(C)(C)C)C2=O)[C@H](O)[C@@H]1O[Si](C)(C)C(C)(C)C	3507.4	Semi standard non polar	33892256
Orotidine,4TBDMS,isomer #4	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C(C(=O)O)=CC(=O)N([Si](C)(C)C(C)(C)C)C2=O)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O[Si](C)(C)C(C)(C)C	3516.1	Semi standard non polar	33892256
Orotidine,4TBDMS,isomer #5	CC(C)(C)[Si](C)(C)OC(=O)C1=CC(=O)N([Si](C)(C)C(C)(C)C)C(=O)N1[C@@H]1O[C@H](CO)[C@@H](O[Si](C)(C)C(C)(C)C)[C@H]1O[Si](C)(C)C(C)(C)C	3521.1	Semi standard non polar	33892256
Orotidine,5TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C(C(=O)O[Si](C)(C)C(C)(C)C)=CC(=O)N([Si](C)(C)C(C)(C)C)C2=O)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O[Si](C)(C)C(C)(C)C	3710.4	Semi standard non polar	33892256
Orotidine,5TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C(C(=O)O[Si](C)(C)C(C)(C)C)=CC(=O)N([Si](C)(C)C(C)(C)C)C2=O)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O[Si](C)(C)C(C)(C)C	3615.4	Standard non polar	33892256
Orotidine,5TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C(C(=O)O[Si](C)(C)C(C)(C)C)=CC(=O)N([Si](C)(C)C(C)(C)C)C2=O)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O[Si](C)(C)C(C)(C)C	3320.0	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Orotidine GC-MS (Non-derivatized) - 70eV, Positive	splash10-05i3-9230000000-e2c457e981d3f20213c6	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Orotidine GC-MS (4 TMS) - 70eV, Positive	splash10-03ei-4340390000-f308e272596bbf4876aa	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Orotidine GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Orotidine GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Orotidine GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Orotidine GC-MS (TMS_1_3) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Orotidine GC-MS (TMS_1_4) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Orotidine GC-MS (TMS_1_5) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Orotidine GC-MS (TMS_2_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Orotidine GC-MS (TMS_2_2) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Orotidine GC-MS (TMS_2_3) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Orotidine GC-MS (TMS_2_4) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Orotidine GC-MS (TMS_2_5) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Orotidine GC-MS (TMS_2_6) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Orotidine GC-MS (TMS_2_7) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Orotidine GC-MS (TMS_2_8) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Orotidine GC-MS (TMS_2_9) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Orotidine GC-MS (TMS_2_10) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Orotidine GC-MS (TMS_3_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Orotidine GC-MS (TMS_3_2) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Orotidine GC-MS (TMS_3_3) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Orotidine GC-MS (TMS_3_4) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Orotidine GC-MS (TMS_3_5) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Orotidine GC-MS (TMS_3_6) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Orotidine GC-MS (TMS_3_7) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Experimental LC-MS/MS	LC-MS/MS Spectrum - Orotidine Quattro_QQQ 10V, Positive-QTOF (Annotated)	splash10-0f92-6790000000-22b02fcae382ac45192a	2012-07-24	HMDB team, MONA	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Orotidine 10V, Positive-QTOF	splash10-0a4r-0940000000-ae1aee48fbe832808af5	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Orotidine 20V, Positive-QTOF	splash10-0a4r-1920000000-8d5291c4fd7f7d30f0bb	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Orotidine 40V, Positive-QTOF	splash10-0aou-8900000000-b3e3dadd94fb667cbb00	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Orotidine 10V, Negative-QTOF	splash10-052o-3970000000-a100d1c804d27c0b6e97	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Orotidine 20V, Negative-QTOF	splash10-0bt9-0910000000-1a9d30040efa9eecd74d	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Orotidine 40V, Negative-QTOF	splash10-01ox-9600000000-001a262ee2894d294d1c	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Orotidine 10V, Positive-QTOF	splash10-000i-0910000000-db12fcd4210da39a9371	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Orotidine 20V, Positive-QTOF	splash10-06ri-0910000000-cb586e3766ceeef71494	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Orotidine 40V, Positive-QTOF	splash10-000i-3900000000-7e74435ea88ec8add7cb	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Orotidine 10V, Negative-QTOF	splash10-000i-0190000000-5c6d124476de69b9c589	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Orotidine 20V, Negative-QTOF	splash10-08fr-1940000000-64fcb770cc2756bd0348	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Orotidine 40V, Negative-QTOF	splash10-0006-9600000000-6b704e1f9de9d9c4d8f6	2021-09-22	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Experimental 1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, experimental)	2021-10-10	Wishart Lab	View Spectrum
Experimental 1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, experimental)	2021-10-10	Wishart Lab	View Spectrum
Experimental 2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 600 MHz, H₂O, experimental)	2012-12-05	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm (predicted from logP)

Biospecimen Locations

Blood
Urine

Tissue Locations

Placenta

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected and Quantified	149.0 +/- 13.0 uM	Adult (>18 years old)	Both	Normal	7877593	details
Blood	Detected and Quantified	4.167 +/- 5.556 uM	Adult (>18 years old)	Both	Normal	12675874	details
Urine	Detected and Quantified	1.12 +/- 0.20 umol/mmol creatinine	Adult (>18 years old)	Both	Normal	Geigy Scientific ...	details
Urine	Detected and Quantified	<0.47 umol/mmol creatinine	Newborn (0-30 days old)	Both	Normal	30817767	details

Abnormal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected and Quantified	70.139 +/- 46.875 uM	Adult (>18 years old)	Both	Uremia	12675874	details
Urine	Detected and Quantified	0.52 umol/mmol creatinine	Adult (>18 years old)	Female	Orotic aciduria I	25757096	details

Associated Disorders and Diseases

Disease References

Uremia
Vanholder R, De Smet R, Glorieux G, Argiles A, Baurmeister U, Brunet P, Clark W, Cohen G, De Deyn PP, Deppisch R, Descamps-Latscha B, Henle T, Jorres A, Lemke HD, Massy ZA, Passlick-Deetjen J, Rodriguez M, Stegmayr B, Stenvinkel P, Tetta C, Wanner C, Zidek W: Review on uremic toxins: classification, concentration, and interindividual variability. Kidney Int. 2003 May;63(5):1934-43. doi: 10.1046/j.1523-1755.2003.00924.x. [PubMed:12675874 ]
Orotic aciduria I
Grohmann K, Lauffer H, Lauenstein P, Hoffmann GF, Seidlitz G: Hereditary orotic aciduria with epilepsy and without megaloblastic anemia. Neuropediatrics. 2015 Apr;46(2):123-5. doi: 10.1055/s-0035-1547341. Epub 2015 Mar 10. [PubMed:25757096 ]

Associated OMIM IDs

258900 (Orotic aciduria I)

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Orotidine

METLIN ID

5754

PubChem Compound

92751

PDB ID

Not Available

ChEBI ID

25722

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

MDB00000252

Good Scents ID

Not Available

References

Synthesis Reference

Curra, William V.; Angle, Robert B. Synthesis of orotidine. Tetrahedron Letters (1963), (8), 533-5.

Material Safety Data Sheet (MSDS)

Download (PDF)

General References

Arranz JA, Riudor E, Rodes M, Roig M, Climent C, Rubio V, Sentis M, Burlina A: Optimization of allopurinol challenge: sample purification, protein intake control, and the use of orotidine response as a discriminative variable improve performance of the test for diagnosing ornithine carbamoyltransferase deficiency. Clin Chem. 1999 Jul;45(7):995-1001. [PubMed:10388475 ]
Harris ML, Oberholzer VG: Conditions affecting the colorimetry of orotic acid and orotidine in urine. Clin Chem. 1980 Mar;26(3):473-9. [PubMed:7363468 ]
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Showing metabocard for Orotidine (HMDB0000788)

MOL for HMDB0000788 (Orotidine)

3D MOL for HMDB0000788 (Orotidine)

3D SDF for HMDB0000788 (Orotidine)

3D-SDF for HMDB0000788 (Orotidine)

PDB for HMDB0000788 (Orotidine)

3D PDB for HMDB0000788 (Orotidine)

SMILES for HMDB0000788 (Orotidine)

INCHI for HMDB0000788 (Orotidine)

Structure for HMDB0000788 (Orotidine)

3D Structure for HMDB0000788 (Orotidine)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra