MiMeDB: Showing metabocard for Orotidine (MMDBc0000368)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2020-12-10 18:36:16 UTC

Update Date

2024-04-30 19:31:56 UTC

Metabolite ID

MMDBc0000368

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>
MMDBc0000368

> <DATABASE_NAME>
MIME

> <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

Synonyms

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

Molecular Formula

C₁₀H₁₂N₂O₈

Average Mass

288.2109

Monoisotopic Mass

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

Not Available

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 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted 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

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-05i3-9230000000-e2c457e981d3f20213c6	2017-09-01	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (4 TMS) - 70eV, Positive	splash10-03ei-4340390000-f308e272596bbf4876aa	2017-10-06	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_4) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_5) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_1) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_2) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_3) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_4) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_5) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_6) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_7) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_8) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_9) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_10) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_1) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_2) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_3) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_4) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_5) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_6) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_7) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)	splash10-0f92-6790000000-22b02fcae382ac45192a	2012-07-24	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0a4r-0940000000-ae1aee48fbe832808af5	2017-09-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0a4r-1920000000-8d5291c4fd7f7d30f0bb	2017-09-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0aou-8900000000-b3e3dadd94fb667cbb00	2017-09-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-052o-3970000000-a100d1c804d27c0b6e97	2017-09-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0bt9-0910000000-1a9d30040efa9eecd74d	2017-09-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-01ox-9600000000-001a262ee2894d294d1c	2017-09-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-000i-0910000000-db12fcd4210da39a9371	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-06ri-0910000000-cb586e3766ceeef71494	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-000i-3900000000-7e74435ea88ec8add7cb	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-000i-0190000000-5c6d124476de69b9c589	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-08fr-1940000000-64fcb770cc2756bd0348	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0006-9600000000-6b704e1f9de9d9c4d8f6	2021-09-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, experimental)		2012-12-04	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, experimental)		2021-10-10	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, experimental)		2021-10-10	View Spectrum
2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 600 MHz, H₂O, experimental)		2012-12-05	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm

Biospecimen Locations

Blood
Placenta
Urine

Tissue Locations

Placenta

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Not Available

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference
Orotic aciduria i		Association	Human Urine	HMDB	25757096
Uremia		Association	Human Blood	HMDB	12675874

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria	Firmicutes	1	Human stool	Indirect association between microbiota composition and metabolites measured in host biospecimen

Exposure Sources

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Units	Age	Sex	Health Condition	Data Source	Reference
Human Urine	Detected and Quantified	0.52		umol/mmol creatinine	Adult (>18 years old)	Female	Orotic aciduria I	HMDB	25757096
Human Blood	Detected and Quantified	70.139	46.875	uM	Adult (>18 years old)	Both	Uremia	HMDB	12675874
Human Urine	Detected and Quantified	<0.47		umol/mmol creatinine	Newborn (0-30 days old)	Both	Normal	HMDB	30817767
Human Blood	Detected and Quantified	149.0	13.0	uM	Adult (>18 years old)	Both	Normal	HMDB	7877593
Human Blood	Detected and Quantified	4.167	5.556	uM	Adult (>18 years old)	Both	Normal	HMDB	12675874
Human Urine	Detected and Quantified	1.12	0.20	umol/mmol creatinine	Adult (>18 years old)	Both	Normal	HMDB	Geigy Scientific Tables, 8th Rev edition, pp. 130. Edited by C. Lentner, West Cadwell, N.J.: Medical education Div., Ciba-Geigy Corp. Basel, Switzerland c1981-1992.
Human Placenta	Detected but not Quantified				Not Specified	Not Specified	Normal	HMDB	34986597

External Links

HMDB ID

HMDB0000788

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

References

Synthesis Reference

Not Available

General References

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 ]
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 ]
MICHELSON AM, DRELL W, MITCHELL HK: A new ribose nucleoside from Neurospora; "orotidine". Proc Natl Acad Sci U S A. 1951 Jul;37(7):396-9. doi: 10.1073/pnas.37.7.396. [PubMed:14853953 ]
van Kuilenburg AB, van Lenthe H, Loffler M, van Gennip AH: Analysis of pyrimidine synthesis "de novo" intermediates in urine and dried urine filter- paper strips with HPLC-electrospray tandem mass spectrometry. Clin Chem. 2004 Nov;50(11):2117-24. doi: 10.1373/clinchem.2004.038869. Epub 2004 Sep 16. [PubMed:15375016 ]
Elshenawy S, Pinney SE, Stuart T, Doulias PT, Zura G, Parry S, Elovitz MA, Bennett MJ, Bansal A, Strauss JF 3rd, Ischiropoulos H, Simmons RA: The Metabolomic Signature of the Placenta in Spontaneous Preterm Birth. Int J Mol Sci. 2020 Feb 4;21(3). pii: ijms21031043. doi: 10.3390/ijms21031043. [PubMed:32033212 ]

Showing metabocard for Orotidine (MMDBc0000368)

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3D MOL for #<Metabolite:0x00007fdb48aab420>

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Structure for #<Metabolite:0x00007fdb48aab420>

3D Structure for #<Metabolite:0x00007fdb48aab420>