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Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References enzymes (1) Show 1 protein XML

Record Information

Version

5.0

Status

Detected and Quantified

Creation Date

2005-11-16 15:48:42 UTC

Update Date

2021-09-14 15:39:00 UTC

HMDB ID

HMDB0000218

Secondary Accession Numbers

HMDB00218

Metabolite Identification

Common Name

Orotidylic acid

Description

Orotidylic acid, also known as orotidylate or 5'-OMP, belongs to the class of organic compounds known as pyrimidine ribonucleoside monophosphates. These are pyrimidine ribobucleotides with monophosphate group linked to the ribose moiety. Orotidylic acid is an extremely weak basic (essentially neutral) compound (based on its pKa). Orotidylic acid exists in all living species, ranging from bacteria to humans. guanidoacetic acid and orotidylic acid can be biosynthesized from glycine and L-arginine; which is catalyzed by the enzyme glycine amidinotransferase, mitochondrial. In humans, orotidylic acid is involved in the metabolic disorder called the dimethylglycine dehydrogenase deficiency pathway. Outside of the human body, Orotidylic acid has been detected, but not quantified in, several different foods, such as parsley, common persimmons, other bread, oriental wheats, and custard apples. This could make orotidylic acid a potential biomarker for the consumption of these foods. A pyrimidine ribonucleoside 5'-monophosphate having 6-carboxyuracil as the nucleobase.

Structure

MOL SDF 3D SDF PDB 3D PDB SMILES InChI


  Mrv1652305122020442D          

 24 25  0  0  0  0            999 V2000
 9999.103610001.9494    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10000.895310001.9412    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10001.366210000.0885    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.3108 9998.8470    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9997.879210001.3257    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10002.080910000.4995    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10000.0258 9999.2613    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9999.3108 9998.0205    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10002.797510000.0885    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
 9996.4477 9998.8470    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10002.3845 9999.3720    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10003.512210000.4995    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10003.2106 9999.3720    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9997.879310000.4994    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9997.164810000.0869    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9997.1648 9999.2618    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9997.8793 9998.8494    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.5938 9999.2618    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.593810000.0869    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9999.983010000.0067    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9999.315610000.4917    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
 9999.570510001.2763    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
10000.395510001.2763    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
10000.650410000.4917    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
  3  6  1  0  0  0  0
  4  7  1  0  0  0  0
  4  8  2  0  0  0  0
  6  9  1  0  0  0  0
  9 11  2  0  0  0  0
  9 12  1  0  0  0  0
  9 13  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 20 21  1  0  0  0  0
 20 24  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 14 19  1  0  0  0  0
 18 19  1  0  0  0  0
 18  4  1  0  0  0  0
 14  5  2  0  0  0  0
 16 10  2  0  0  0  0
 22  1  1  6  0  0  0
 21 19  1  1  0  0  0
 23  2  1  6  0  0  0
 24  3  1  1  0  0  0
M  END
> <DATABASE_ID>
HMDB0000218

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C10H13N2O11P/c13-5-1-3(9(16)17)12(10(18)11-5)8-7(15)6(14)4(23-8)2-22-24(19,20)21/h1,4,6-8,14-15H,2H2,(H,16,17)(H,11,13,18)(H2,19,20,21)/t4-,6-,7-,8-/m1/s1

> <INCHI_KEY>
KYOBSHFOBAOFBF-XVFCMESISA-N

> <FORMULA>
C10H13N2O11P

> <MOLECULAR_WEIGHT>
368.1908

> <EXACT_MASS>
368.02569578

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
37

> <JCHEM_AVERAGE_POLARIZABILITY>
29.646566664527832

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-1.67

> <JCHEM_LOGP>
-2.911181674

> <ALOGPS_LOGS>
-1.63

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-3

> <JCHEM_PKA>
2.8807694070808423

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.21301296157929

> <JCHEM_PKA_STRONGEST_BASIC>
-3.6645573647317757

> <JCHEM_POLAR_SURFACE_AREA>
203.16

> <JCHEM_REFRACTIVITY>
70.7438

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
8.61e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
6-carboxy-5'-uridylic acid

> <JCHEM_VEBER_RULE>
0

$$$$

https://cactus.nci.nih.gov/chemical/structure/O%5BC@H%5D1%5BC@@H%5D(O)%5BC@@H...
 OpenBabel09142113213D
Jmol version 14.31.45  2021-07-21 05:08 EXTRACT: ({0:36})
 37 38  0  0  0  0  0  0  0  0999 V2000
   -0.7018    3.3797   -1.0174 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5051    1.9732   -1.1762 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.8545    1.6479   -2.1562 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9843    1.6097   -0.9844 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.3706    1.1026   -1.8685 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7535    2.7810   -0.7044 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9843    0.6553    0.2303 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.1839    1.2090    1.1478 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3468    0.0959    0.2601 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2319    1.1952   -0.0569 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.3729    1.8326    0.8160 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5797    0.6680   -0.5534 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2484   -0.0088    0.5128 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6969   -0.6917    0.3461 P   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0824   -1.4701    1.7016 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7960    0.4470    0.0500 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6636   -1.6502   -0.7810 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9807   -0.4030    0.0474 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6119   -1.5663   -0.5137 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4558   -1.7164   -0.8591 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4870   -2.5692   -0.7040 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.7761   -2.4311   -0.3308 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5705   -3.3368   -0.5017 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2038   -1.1687    0.2850 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2812   -0.1849    0.4491 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6669    1.1069    1.0655 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9518    1.3380    1.3968 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8248    1.9566    1.2716 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2429    3.9179   -1.6768 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7382    3.4400   -1.4119 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1924    1.5019   -0.8954 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4167   -0.0256   -1.3784 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9448   -1.9066    1.6728 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8723    1.1112    0.7486 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1895   -3.3974   -1.1120 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2278   -1.0241    0.5960 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1549    2.1949    1.7961 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1 29  1  0  0  0  0
  2  3  1  6  0  0  0
  2  4  1  0  0  0  0
  2 10  1  0  0  0  0
  4  5  1  6  0  0  0
  4  6  1  0  0  0  0
  4  7  1  0  0  0  0
  6 30  1  0  0  0  0
  7  8  1  1  0  0  0
  7  9  1  0  0  0  0
  7 18  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  1  0  0  0
 10 12  1  0  0  0  0
 12 13  1  0  0  0  0
 12 31  1  0  0  0  0
 12 32  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 14 16  1  0  0  0  0
 14 17  2  0  0  0  0
 15 33  1  0  0  0  0
 16 34  1  0  0  0  0
 18 19  1  0  0  0  0
 18 25  1  0  0  0  0
 19 20  2  0  0  0  0
 19 21  1  0  0  0  0
 21 22  1  0  0  0  0
 21 35  1  0  0  0  0
 22 23  2  0  0  0  0
 22 24  1  0  0  0  0
 24 25  2  0  0  0  0
 24 36  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 26 28  2  0  0  0  0
 27 37  1  0  0  0  0
M  END
$$$$

HEADER    PROTEIN                                 12-MAY-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   12-MAY-20         0                                  
HETATM    1  O   UNK     0    8664.9938670.306   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0    8668.3388670.290   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0    8669.2178666.832   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0    8665.3808664.514   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0    8662.7088669.141   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0    8670.5518667.599   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0    8666.7158665.288   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0    8665.3808662.972   0.000  0.00  0.00           O+0
HETATM    9  P   UNK     0    8671.8898666.832   0.000  0.00  0.00           P+0
HETATM   10  O   UNK     0    8660.0368664.514   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0    8671.1188665.494   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0    8673.2238667.599   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0    8672.6608665.494   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0    8662.7088667.599   0.000  0.00  0.00           C+0
HETATM   15  N   UNK     0    8661.3748666.829   0.000  0.00  0.00           N+0
HETATM   16  C   UNK     0    8661.3748665.289   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0    8662.7088664.519   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0    8664.0428665.289   0.000  0.00  0.00           C+0
HETATM   19  N   UNK     0    8664.0428666.829   0.000  0.00  0.00           N+0
HETATM   20  O   UNK     0    8666.6358666.679   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0    8665.3898667.585   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0    8665.8658669.049   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0    8667.4058669.049   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0    8667.8818667.585   0.000  0.00  0.00           C+0
CONECT    1   22                                                            
CONECT    2   23                                                            
CONECT    3    6   24                                                       
CONECT    4    7    8   18                                                  
CONECT    5   14                                                            
CONECT    6    3    9                                                       
CONECT    7    4                                                            
CONECT    8    4                                                            
CONECT    9    6   11   12   13                                             
CONECT   10   16                                                            
CONECT   11    9                                                            
CONECT   12    9                                                            
CONECT   13    9                                                            
CONECT   14   15   19    5                                                  
CONECT   15   14   16                                                       
CONECT   16   17   15   10                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19    4                                                  
CONECT   19   14   18   21                                                  
CONECT   20   21   24                                                       
CONECT   21   22   20   19                                                  
CONECT   22   21   23    1                                                  
CONECT   23   22   24    2                                                  
CONECT   24   23   20    3                                                  
MASTER        0    0    0    0    0    0    0    0   24    0   50    0
END

COMPND    https://cactus.nci.nih.gov/chemical/structure/O%5BC@H%5D1%5BC@@H%5D(O)%5BC@@H... 
AUTHOR    GENERATED BY OPEN BABEL 3.1.0
HETATM    1  O   UNL     1      -0.702   3.380  -1.017  1.00  0.00           O  
HETATM    2  C   UNL     1      -0.505   1.973  -1.176  1.00  0.00           C  
HETATM    3  H   UNL     1      -0.855   1.648  -2.156  1.00  0.00           H  
HETATM    4  C   UNL     1       0.984   1.610  -0.984  1.00  0.00           C  
HETATM    5  H   UNL     1       1.371   1.103  -1.869  1.00  0.00           H  
HETATM    6  O   UNL     1       1.754   2.781  -0.704  1.00  0.00           O  
HETATM    7  C   UNL     1       0.984   0.655   0.230  1.00  0.00           C  
HETATM    8  H   UNL     1       1.184   1.209   1.148  1.00  0.00           H  
HETATM    9  O   UNL     1      -0.347   0.096   0.260  1.00  0.00           O  
HETATM   10  C   UNL     1      -1.232   1.195  -0.057  1.00  0.00           C  
HETATM   11  H   UNL     1      -1.373   1.833   0.816  1.00  0.00           H  
HETATM   12  C   UNL     1      -2.580   0.668  -0.553  1.00  0.00           C  
HETATM   13  O   UNL     1      -3.248  -0.009   0.513  1.00  0.00           O  
HETATM   14  P   UNL     1      -4.697  -0.692   0.346  1.00  0.00           P  
HETATM   15  O   UNL     1      -5.082  -1.470   1.702  1.00  0.00           O  
HETATM   16  O   UNL     1      -5.796   0.447   0.050  1.00  0.00           O  
HETATM   17  O   UNL     1      -4.664  -1.650  -0.781  1.00  0.00           O  
HETATM   18  N   UNL     1       1.981  -0.403   0.047  1.00  0.00           N  
HETATM   19  C   UNL     1       1.612  -1.566  -0.514  1.00  0.00           C  
HETATM   20  O   UNL     1       0.456  -1.716  -0.859  1.00  0.00           O  
HETATM   21  N   UNL     1       2.487  -2.569  -0.704  1.00  0.00           N  
HETATM   22  C   UNL     1       3.776  -2.431  -0.331  1.00  0.00           C  
HETATM   23  O   UNL     1       4.571  -3.337  -0.502  1.00  0.00           O  
HETATM   24  C   UNL     1       4.204  -1.169   0.285  1.00  0.00           C  
HETATM   25  C   UNL     1       3.281  -0.185   0.449  1.00  0.00           C  
HETATM   26  C   UNL     1       3.667   1.107   1.065  1.00  0.00           C  
HETATM   27  O   UNL     1       4.952   1.338   1.397  1.00  0.00           O  
HETATM   28  O   UNL     1       2.825   1.957   1.272  1.00  0.00           O  
HETATM   29  H   UNL     1      -0.243   3.918  -1.677  1.00  0.00           H  
HETATM   30  H   UNL     1       1.738   3.440  -1.412  1.00  0.00           H  
HETATM   31  H   UNL     1      -3.192   1.502  -0.895  1.00  0.00           H  
HETATM   32  H   UNL     1      -2.417  -0.026  -1.378  1.00  0.00           H  
HETATM   33  H   UNL     1      -5.945  -1.907   1.673  1.00  0.00           H  
HETATM   34  H   UNL     1      -5.872   1.111   0.749  1.00  0.00           H  
HETATM   35  H   UNL     1       2.189  -3.397  -1.112  1.00  0.00           H  
HETATM   36  H   UNL     1       5.228  -1.024   0.596  1.00  0.00           H  
HETATM   37  H   UNL     1       5.155   2.195   1.796  1.00  0.00           H  
CONECT    1    2   29                                                 
CONECT    2    1    3    4   10                                       
CONECT    3    2                                                      
CONECT    4    2    5    6    7                                       
CONECT    5    4                                                      
CONECT    6    4   30                                                 
CONECT    7    4    8    9   18                                       
CONECT    8    7                                                      
CONECT    9    7   10                                                 
CONECT   10    9   11    2   12                                       
CONECT   11   10                                                      
CONECT   12   10   13   31   32                                       
CONECT   13   12   14                                                 
CONECT   14   13   15   16   17                                       
CONECT   14   17                                                      
CONECT   15   14   33                                                 
CONECT   16   14   34                                                 
CONECT   17   14   14                                                 
CONECT   18    7   19   25                                            
CONECT   19   18   20   20   21                                       
CONECT   20   19   19                                                 
CONECT   21   19   22   35                                            
CONECT   22   21   23   23   24                                       
CONECT   23   22   22                                                 
CONECT   24   22   25   25   36                                       
CONECT   25   24   24   18   26                                       
CONECT   26   25   27   28   28                                       
CONECT   27   26   37                                                 
CONECT   28   26   26                                                 
CONECT   29    1                                                      
CONECT   30    6                                                      
CONECT   31   12                                                      
CONECT   32   12                                                      
CONECT   33   15                                                      
CONECT   34   16                                                      
CONECT   35   21                                                      
CONECT   36   24                                                      
CONECT   37   27                                                      
MASTER        0    0    0    0    0    0    0    0   37    0   37    0
END

https://cactus.nci.nih.gov/chemical/structure/O%5BC@H%5D1%5BC@@H%5D(O)%5BC@@H...
 OpenBabel09142113213D
Jmol version 14.31.45  2021-07-21 05:08 EXTRACT: ({0:36})
 37 38  0  0  0  0  0  0  0  0999 V2000
   -0.7018    3.3797   -1.0174 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5051    1.9732   -1.1762 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.8545    1.6479   -2.1562 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9843    1.6097   -0.9844 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.3706    1.1026   -1.8685 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7535    2.7810   -0.7044 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9843    0.6553    0.2303 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.1839    1.2090    1.1478 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3468    0.0959    0.2601 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2319    1.1952   -0.0569 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.3729    1.8326    0.8160 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5797    0.6680   -0.5534 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2484   -0.0088    0.5128 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6969   -0.6917    0.3461 P   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0824   -1.4701    1.7016 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7960    0.4470    0.0500 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6636   -1.6502   -0.7810 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9807   -0.4030    0.0474 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6119   -1.5663   -0.5137 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4558   -1.7164   -0.8591 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4870   -2.5692   -0.7040 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.7761   -2.4311   -0.3308 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5705   -3.3368   -0.5017 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2038   -1.1687    0.2850 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2812   -0.1849    0.4491 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6669    1.1069    1.0655 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9518    1.3380    1.3968 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8248    1.9566    1.2716 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2429    3.9179   -1.6768 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7382    3.4400   -1.4119 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1924    1.5019   -0.8954 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4167   -0.0256   -1.3784 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9448   -1.9066    1.6728 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8723    1.1112    0.7486 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1895   -3.3974   -1.1120 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2278   -1.0241    0.5960 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1549    2.1949    1.7961 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1 29  1  0  0  0  0
  2  3  1  6  0  0  0
  2  4  1  0  0  0  0
  2 10  1  0  0  0  0
  4  5  1  6  0  0  0
  4  6  1  0  0  0  0
  4  7  1  0  0  0  0
  6 30  1  0  0  0  0
  7  8  1  1  0  0  0
  7  9  1  0  0  0  0
  7 18  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  1  0  0  0
 10 12  1  0  0  0  0
 12 13  1  0  0  0  0
 12 31  1  0  0  0  0
 12 32  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 14 16  1  0  0  0  0
 14 17  2  0  0  0  0
 15 33  1  0  0  0  0
 16 34  1  0  0  0  0
 18 19  1  0  0  0  0
 18 25  1  0  0  0  0
 19 20  2  0  0  0  0
 19 21  1  0  0  0  0
 21 22  1  0  0  0  0
 21 35  1  0  0  0  0
 22 23  2  0  0  0  0
 22 24  1  0  0  0  0
 24 25  2  0  0  0  0
 24 36  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 26 28  2  0  0  0  0
 27 37  1  0  0  0  0
M  END
$$$$

View in JSmol View Stereo Labels

Synonyms

Value	Source
6-Carboxy-5'-uridylic acid	ChEBI
Orotidine 5'-(dihydrogen phosphate)	ChEBI
6-Carboxy-5'-uridylate	Generator
Orotidine 5'-(dihydrogen phosphoric acid)	Generator
Orotidylate	Generator
1,2,3,6-Tetrahydro-2,6-dioxo-3-(5-O-phosphono-b-D-ribofuranosyl)-4-pyrimidinecarboxylate	HMDB
1,2,3,6-Tetrahydro-2,6-dioxo-3-(5-O-phosphono-b-D-ribofuranosyl)-4-pyrimidinecarboxylic acid	HMDB
1,2,3,6-Tetrahydro-2,6-dioxo-3-(5-O-phosphono-beta-delta-ribofuranosyl)-4-pyrimidinecarboxylate	HMDB
1,2,3,6-Tetrahydro-2,6-dioxo-3-(5-O-phosphono-beta-delta-ribofuranosyl)-4-pyrimidinecarboxylic acid	HMDB
2,6-Dioxo-3-(5-O-phosphono-beta-D-ribofuranosyl)-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid	HMDB
2,6-Dioxo-3-(5-O-phosphono-beta-delta-ribofuranosyl)-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid	HMDB
5'-(Dihydrogen phosphate) 6-carboxy-uridine	HMDB
5'-(Dihydrogen phosphate) orotidine	HMDB
5'-OMP	HMDB
5'-Phosphate orotidine	HMDB
5-(Dihydrogen phosphate)orotidine	HMDB
Ometoprim	HMDB
OMP	HMDB
Omp (nucleotide)	HMDB
Orotidine 5'-monophosphate	HMDB
Orotidine 5'-phosphate	HMDB
Orotidine monophosphate	HMDB
Orotidine-5'-phosphate	HMDB
1,2,3,6-Tetrahydro-2,6-dioxo-3-(5-O-phosphono-beta-D-ribofuranosyl)-4-pyrimidinecarboxylic acid	HMDB
1,2,3,6-Tetrahydro-2,6-dioxo-3-(5-O-phosphono-β-D-ribofuranosyl)-4-pyrimidinecarboxylic acid	HMDB
5’-OMP	HMDB
Orotidine 5’-monophosphate	HMDB
Orotidylic acid	HMDB

Chemical Formula

C₁₀H₁₃N₂O₁₁P

Average Molecular Weight

368.1908

Monoisotopic Molecular Weight

368.02569578

IUPAC Name

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

Traditional Name

6-carboxy-5'-uridylic acid

CAS Registry Number

2149-82-8

SMILES

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

InChI Identifier

InChI=1S/C10H13N2O11P/c13-5-1-3(9(16)17)12(10(18)11-5)8-7(15)6(14)4(23-8)2-22-24(19,20)21/h1,4,6-8,14-15H,2H2,(H,16,17)(H,11,13,18)(H2,19,20,21)/t4-,6-,7-,8-/m1/s1

InChI Key

KYOBSHFOBAOFBF-XVFCMESISA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyrimidine ribonucleoside monophosphates. These are pyrimidine ribobucleotides with monophosphate group linked to the ribose moiety.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Pyrimidine nucleotides

Sub Class

Pyrimidine ribonucleotides

Direct Parent

Pyrimidine ribonucleoside monophosphates

Alternative Parents

Substituents

Pyrimidine ribonucleoside monophosphate
Pentose-5-phosphate
Pentose phosphate
Glycosyl compound
N-glycosyl compound
Monosaccharide phosphate
Pentose monosaccharide
Pyrimidine-6-carboxylic acid or derivatives
Pyrimidine-6-carboxylic acid
Hydropyrimidine carboxylic acid derivative
Monoalkyl phosphate
Pyrimidone
Hydropyrimidine
Monosaccharide
Organic phosphoric acid derivative
Pyrimidine
Alkyl phosphate
Phosphoric acid ester
Heteroaromatic compound
Vinylogous amide
Tetrahydrofuran
Secondary alcohol
Urea
Lactam
1,2-diol
Organoheterocyclic compound
Carboxylic acid derivative
Carboxylic acid
Azacycle
Monocarboxylic acid or derivatives
Oxacycle
Organic oxide
Organopnictogen compound
Organic oxygen compound
Alcohol
Hydrocarbon derivative
Organooxygen compound
Organic nitrogen compound
Organonitrogen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

pyrimidine ribonucleoside 5'-monophosphate (CHEBI:15842 )

Ontology

Disposition

Source:

Endogenous

Biological location:

Subcellular:

Cytoplasm

Organ and components:

Prostate

Process

Naturally occurring process:

Biological process:

Biochemical pathway:

Role

Industrial application:

Pharmaceutical industry:

Pharmaceutical

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

Predicted Molecular Properties

Property	Value	Source
Water Solubility	8.61 g/L	ALOGPS
logP	-1.7	ALOGPS
logP	-2.9	ChemAxon
logS	-1.6	ALOGPS
pKa (Strongest Acidic)	1.21	ChemAxon
pKa (Strongest Basic)	-3.7	ChemAxon
Physiological Charge	-3	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	203.16 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	70.74 m³·mol⁻¹	ChemAxon
Polarizability	29.65 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Spectral Properties

Collision Cross Sections

Name	Adduct	Type	Data Source	Value	Reference
DarkChem	[M+H]+	Predicted	Not Available	180.181	31661259
DarkChem	[M-H]-	Predicted	Not Available	172.636	31661259
AllCCS	[M+H]+	Predicted	Not Available	176.32	32859911
AllCCS	[M-H]-	Predicted	Not Available	170.504	32859911

Retention Indices

Underivatized

Not Available

Derivatized

Derivative	Value	Reference
Orotidylic acid,1TMS,#1	2871.0022	https://arxiv.org/abs/1905.12712
Orotidylic acid,1TMS,#2	2845.778	https://arxiv.org/abs/1905.12712
Orotidylic acid,1TMS,#3	2780.0342	https://arxiv.org/abs/1905.12712
Orotidylic acid,1TMS,#4	3026.3608	https://arxiv.org/abs/1905.12712
Orotidylic acid,1TMS,#5	3003.8823	https://arxiv.org/abs/1905.12712
Orotidylic acid,2TMS,#1	2718.011	https://arxiv.org/abs/1905.12712
Orotidylic acid,2TMS,#2	2797.1465	https://arxiv.org/abs/1905.12712
Orotidylic acid,2TMS,#3	2966.8555	https://arxiv.org/abs/1905.12712
Orotidylic acid,2TMS,#4	2931.8916	https://arxiv.org/abs/1905.12712
Orotidylic acid,2TMS,#5	2697.4001	https://arxiv.org/abs/1905.12712
Orotidylic acid,2TMS,#6	2955.0269	https://arxiv.org/abs/1905.12712
Orotidylic acid,2TMS,#7	2912.7585	https://arxiv.org/abs/1905.12712
Orotidylic acid,2TMS,#8	2891.5771	https://arxiv.org/abs/1905.12712
Orotidylic acid,2TMS,#9	2849.6401	https://arxiv.org/abs/1905.12712
Orotidylic acid,2TMS,#10	3019.5564	https://arxiv.org/abs/1905.12712
Orotidylic acid,2TMS,#11	3069.3777	https://arxiv.org/abs/1905.12712
Orotidylic acid,3TMS,#1	2697.9585	https://arxiv.org/abs/1905.12712
Orotidylic acid,3TMS,#2	2861.1277	https://arxiv.org/abs/1905.12712
Orotidylic acid,3TMS,#3	2810.6704	https://arxiv.org/abs/1905.12712
Orotidylic acid,3TMS,#4	2911.3252	https://arxiv.org/abs/1905.12712
Orotidylic acid,3TMS,#5	2892.3162	https://arxiv.org/abs/1905.12712
Orotidylic acid,3TMS,#6	2964.2888	https://arxiv.org/abs/1905.12712
Orotidylic acid,3TMS,#7	2995.75	https://arxiv.org/abs/1905.12712
Orotidylic acid,3TMS,#8	2841.5442	https://arxiv.org/abs/1905.12712
Orotidylic acid,3TMS,#9	2794.8052	https://arxiv.org/abs/1905.12712
Orotidylic acid,3TMS,#10	2952.666	https://arxiv.org/abs/1905.12712
Orotidylic acid,3TMS,#11	2987.617	https://arxiv.org/abs/1905.12712
Orotidylic acid,3TMS,#12	2925.722	https://arxiv.org/abs/1905.12712
Orotidylic acid,3TMS,#13	2924.5205	https://arxiv.org/abs/1905.12712
Orotidylic acid,3TMS,#14	3033.4412	https://arxiv.org/abs/1905.12712
Orotidylic acid,1TBDMS,#1	3103.1904	https://arxiv.org/abs/1905.12712
Orotidylic acid,1TBDMS,#2	3078.8223	https://arxiv.org/abs/1905.12712
Orotidylic acid,1TBDMS,#3	3056.6887	https://arxiv.org/abs/1905.12712
Orotidylic acid,1TBDMS,#4	3244.0117	https://arxiv.org/abs/1905.12712
Orotidylic acid,1TBDMS,#5	3195.659	https://arxiv.org/abs/1905.12712
Orotidylic acid,2TBDMS,#1	3180.7026	https://arxiv.org/abs/1905.12712
Orotidylic acid,2TBDMS,#2	3221.502	https://arxiv.org/abs/1905.12712
Orotidylic acid,2TBDMS,#3	3382.0776	https://arxiv.org/abs/1905.12712
Orotidylic acid,2TBDMS,#4	3362.9883	https://arxiv.org/abs/1905.12712
Orotidylic acid,2TBDMS,#5	3158.5486	https://arxiv.org/abs/1905.12712
Orotidylic acid,2TBDMS,#6	3372.13	https://arxiv.org/abs/1905.12712
Orotidylic acid,2TBDMS,#7	3343.9973	https://arxiv.org/abs/1905.12712
Orotidylic acid,2TBDMS,#8	3357.4685	https://arxiv.org/abs/1905.12712
Orotidylic acid,2TBDMS,#9	3322.192	https://arxiv.org/abs/1905.12712
Orotidylic acid,2TBDMS,#10	3443.665	https://arxiv.org/abs/1905.12712
Orotidylic acid,2TBDMS,#11	3470.8667	https://arxiv.org/abs/1905.12712
Orotidylic acid,3TBDMS,#1	3376.5068	https://arxiv.org/abs/1905.12712
Orotidylic acid,3TBDMS,#2	3532.0076	https://arxiv.org/abs/1905.12712
Orotidylic acid,3TBDMS,#3	3505.1404	https://arxiv.org/abs/1905.12712
Orotidylic acid,3TBDMS,#4	3523.619	https://arxiv.org/abs/1905.12712
Orotidylic acid,3TBDMS,#5	3537.7988	https://arxiv.org/abs/1905.12712
Orotidylic acid,3TBDMS,#6	3593.544	https://arxiv.org/abs/1905.12712
Orotidylic acid,3TBDMS,#7	3637.9526	https://arxiv.org/abs/1905.12712
Orotidylic acid,3TBDMS,#8	3528.0222	https://arxiv.org/abs/1905.12712
Orotidylic acid,3TBDMS,#9	3491.986	https://arxiv.org/abs/1905.12712
Orotidylic acid,3TBDMS,#10	3595.6921	https://arxiv.org/abs/1905.12712
Orotidylic acid,3TBDMS,#11	3633.1458	https://arxiv.org/abs/1905.12712
Orotidylic acid,3TBDMS,#12	3590.9976	https://arxiv.org/abs/1905.12712
Orotidylic acid,3TBDMS,#13	3606.523	https://arxiv.org/abs/1905.12712
Orotidylic acid,3TBDMS,#14	3680.1108	https://arxiv.org/abs/1905.12712

Spectra

GC-MS

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0002-9512000000-a3f8062edabfeda1eaa8	2017-09-01	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positive	splash10-0002-9221230000-0c722324f49458fdfb65	2017-10-06	View Spectrum

LC-MS/MS

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0a4i-0914000000-3337770bad1b3ba8486c	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0a4i-1911000000-f94acf2aa5da3364c517	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a4l-5900000000-81a1aba75871162fc05b	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0axv-8917000000-d1de3bc4514e88dd288c	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-056r-9701000000-13540f203bff602cb8f5	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9200000000-2bf7c464e9b79ae5c6a9	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-014i-2009000000-9ea216a0949682e0fe1f	2021-09-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9101000000-fef21032aec9be94593f	2021-09-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9200000000-8b5f1e6eeb57e5800b69	2021-09-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-01b9-0977000000-d51bb310da0232d1c1bb	2021-09-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0cdi-0930000000-504b86c3d067b5715b14	2021-09-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-05mk-4900000000-c8b6c09c13fc530cdcc4	2021-09-09	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm

Biospecimen Locations

Prostate Tissue

Tissue Locations

Prostate

Pathways

Name	SMPDB/Pathwhiz	KEGG
Pyrimidine Metabolism
Beta Ureidopropionase Deficiency		Not Available
UMP Synthase Deficiency (Orotic Aciduria)		Not Available
Dihydropyrimidinase Deficiency		Not Available
MNGIE (Mitochondrial Neurogastrointestinal Encephalopathy)		Not Available

Normal Concentrations

Not Available

Abnormal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Prostate Tissue	Detected and Quantified	0.5 (0.0-1.0) umol/g tissue	Adult (>18 years old)	Both	Prostate Cancer	19212411	details

Associated Disorders and Diseases

Disease References

Prostate cancer

Sreekumar A, Poisson LM, Rajendiran TM, Khan AP, Cao Q, Yu J, Laxman B, Mehra R, Lonigro RJ, Li Y, Nyati MK, Ahsan A, Kalyana-Sundaram S, Han B, Cao X, Byun J, Omenn GS, Ghosh D, Pennathur S, Alexander DC, Berger A, Shuster JR, Wei JT, Varambally S, Beecher C, Chinnaiyan AM: Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression. Nature. 2009 Feb 12;457(7231):910-4. doi: 10.1038/nature07762. [PubMed:19212411 ]

Associated OMIM IDs

176807 (Prostate cancer)

External Links

DrugBank ID

DB02957

Phenol Explorer Compound ID

Not Available

FooDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

OROTIDINE-5-PHOSPHATE

BiGG ID

36813

Wikipedia Link

Orotidine 5'-monophosphate

METLIN ID

5228

PubChem Compound

160617

PDB ID

Not Available

ChEBI ID

15842

Food Biomarker Ontology

Not Available

VMH ID

OROT5P

MarkerDB ID

Not Available

References

Synthesis Reference

Ueda, Tohru; Yamamoto, Miyako; Yamane, Akira; Imazawa, Masaoki; Inoue, Hideo. Nucleosides and nucleotides. XXIII. Conversion of uridine nucleotides to the 6-cyano derivatives: synthesis of orotidylic acid. Journal of Carbohydrates, Nucleosides, Nucleotides (1978), 5(3), 261-71.

Material Safety Data Sheet (MSDS)

Not Available

General References

Traut TW: Uridine-5'-phosphate synthase: evidence for substrate cycling involving this bifunctional protein. Arch Biochem Biophys. 1989 Jan;268(1):108-15. [PubMed:2912371 ]
Sreekumar A, Poisson LM, Rajendiran TM, Khan AP, Cao Q, Yu J, Laxman B, Mehra R, Lonigro RJ, Li Y, Nyati MK, Ahsan A, Kalyana-Sundaram S, Han B, Cao X, Byun J, Omenn GS, Ghosh D, Pennathur S, Alexander DC, Berger A, Shuster JR, Wei JT, Varambally S, Beecher C, Chinnaiyan AM: Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression. Nature. 2009 Feb 12;457(7231):910-4. doi: 10.1038/nature07762. [PubMed:19212411 ]

Enzymes

Enzyme Details

1. Uridine 5'-monophosphate synthase

General function:: Involved in catalytic activity
Specific function:: Not Available
Gene Name:: UMPS
Uniprot ID:: P11172
Molecular weight:: 52221.075

Reactions

Orotidylic acid + Pyrophosphate → Orotic acid + Phosphoribosyl pyrophosphate	details
Orotidylic acid → Uridine 5'-monophosphate + CO(2)	details
Orotidylic acid → Uridine 5'-monophosphate + Carbon dioxide	details

Showing metabocard for Orotidylic acid (HMDB0000218)

MOL for HMDB0000218 (Orotidylic acid)

3D MOL for HMDB0000218 (Orotidylic acid)

3D SDF for HMDB0000218 (Orotidylic acid)

3D-SDF for HMDB0000218 (Orotidylic acid)

PDB for HMDB0000218 (Orotidylic acid)

3D PDB for HMDB0000218 (Orotidylic acid)

SMILES for HMDB0000218 (Orotidylic acid)

INCHI for HMDB0000218 (Orotidylic acid)

Structure for HMDB0000218 (Orotidylic acid)

3D Structure for HMDB0000218 (Orotidylic acid)

Collision Cross Sections

Retention Indices

Underivatized

Derivatized

GC-MS

LC-MS/MS

Enzymes

Reactions