NP-MRD: Showing NP-Card for Orotidine (NP0000088)

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Record Information

Version

2.0

Created at

2005-11-16 15:48:42 UTC

Updated at

2021-08-16 18:04:13 UTC

NP-MRD ID

NP0000088

Secondary Accession Numbers

None

Natural Product 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


  Mrv1652306242117433D          

 32 33  0  0  0  0            999 V2000
   -2.8840   -2.1551    2.2494 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9489   -1.5762    1.6121 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7532   -2.2231    1.5956 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1923   -0.3225    0.9695 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4991    0.2141    1.0856 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7947    1.4070    0.4950 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9571    1.9355    0.5688 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8235    2.0380   -0.1841 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5895    1.5210   -0.2877 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7080    2.1502   -0.9365 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2545    0.3177    0.2960 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0610   -0.1252    0.1232 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.9558    1.0062   -0.0504 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1489    0.2884   -0.1182 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.3005    1.1516   -0.5698 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.4186    2.1816    0.3724 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8787   -0.8379   -1.1219 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.2708   -2.0211   -0.5326 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3583   -0.7828   -1.2043 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.2139   -2.0184   -1.3839 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5533   -3.1094    1.1481 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2381   -0.3348    1.6419 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0696    2.9497   -0.6288 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5666   -0.6833    0.9093 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3276   -0.1306    0.8931 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2557    0.6018   -0.5633 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0594    1.6264   -1.5263 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2530    2.0998    0.9051 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3502   -0.6362   -2.0888 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7658   -1.8691    0.3213 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1103   -0.0757   -2.0455 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3986   -2.5877   -1.9441 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 14 17  1  0  0  0  0
 17 18  1  0  0  0  0
 17 19  1  0  0  0  0
 19 20  1  0  0  0  0
 11  4  1  0  0  0  0
 19 12  1  0  0  0  0
  3 21  1  0  0  0  0
  5 22  1  0  0  0  0
  8 23  1  0  0  0  0
 12 24  1  1  0  0  0
 14 25  1  1  0  0  0
 15 26  1  0  0  0  0
 15 27  1  0  0  0  0
 16 28  1  0  0  0  0
 17 29  1  6  0  0  0
 18 30  1  0  0  0  0
 19 31  1  6  0  0  0
 20 32  1  0  0  0  0
M  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


  Mrv1652306242117433D          

 32 33  0  0  0  0            999 V2000
   -2.8840   -2.1551    2.2494 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9489   -1.5762    1.6121 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7532   -2.2231    1.5956 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1923   -0.3225    0.9695 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4991    0.2141    1.0856 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7947    1.4070    0.4950 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9571    1.9355    0.5688 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8235    2.0380   -0.1841 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5895    1.5210   -0.2877 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7080    2.1502   -0.9365 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2545    0.3177    0.2960 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0610   -0.1252    0.1232 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.9558    1.0062   -0.0504 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1489    0.2884   -0.1182 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.3005    1.1516   -0.5698 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.4186    2.1816    0.3724 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8787   -0.8379   -1.1219 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.2708   -2.0211   -0.5326 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3583   -0.7828   -1.2043 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.2139   -2.0184   -1.3839 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5533   -3.1094    1.1481 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2381   -0.3348    1.6419 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0696    2.9497   -0.6288 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5666   -0.6833    0.9093 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3276   -0.1306    0.8931 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2557    0.6018   -0.5633 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0594    1.6264   -1.5263 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2530    2.0998    0.9051 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3502   -0.6362   -2.0888 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7658   -1.8691    0.3213 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1103   -0.0757   -2.0455 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3986   -2.5877   -1.9441 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 14 17  1  0  0  0  0
 17 18  1  0  0  0  0
 17 19  1  0  0  0  0
 19 20  1  0  0  0  0
 11  4  1  0  0  0  0
 19 12  1  0  0  0  0
  3 21  1  0  0  0  0
  5 22  1  0  0  0  0
  8 23  1  0  0  0  0
 12 24  1  1  0  0  0
 14 25  1  1  0  0  0
 15 26  1  0  0  0  0
 15 27  1  0  0  0  0
 16 28  1  0  0  0  0
 17 29  1  6  0  0  0
 18 30  1  0  0  0  0
 19 31  1  6  0  0  0
 20 32  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0000088

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]OC(=O)C1=C([H])C(=O)N([H])C(=O)N1[C@]1([H])O[C@]([H])(C([H])([H])O[H])[C@@]([H])(O[H])[C@@]1([H])O[H]

> <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                                 24-JUN-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-JUN-21         0                                  
HETATM    1  O   UNK     0      -2.884  -2.155   2.249  0.00  0.00           O+0
HETATM    2  C   UNK     0      -1.949  -1.576   1.612  0.00  0.00           C+0
HETATM    3  O   UNK     0      -0.753  -2.223   1.596  0.00  0.00           O+0
HETATM    4  C   UNK     0      -2.192  -0.323   0.970  0.00  0.00           C+0
HETATM    5  C   UNK     0      -3.499   0.214   1.086  0.00  0.00           C+0
HETATM    6  C   UNK     0      -3.795   1.407   0.495  0.00  0.00           C+0
HETATM    7  O   UNK     0      -4.957   1.936   0.569  0.00  0.00           O+0
HETATM    8  N   UNK     0      -2.824   2.038  -0.184  0.00  0.00           N+0
HETATM    9  C   UNK     0      -1.589   1.521  -0.288  0.00  0.00           C+0
HETATM   10  O   UNK     0      -0.708   2.150  -0.937  0.00  0.00           O+0
HETATM   11  N   UNK     0      -1.254   0.318   0.296  0.00  0.00           N+0
HETATM   12  C   UNK     0       0.061  -0.125   0.123  0.00  0.00           C+0
HETATM   13  O   UNK     0       0.956   1.006  -0.050  0.00  0.00           O+0
HETATM   14  C   UNK     0       2.149   0.288  -0.118  0.00  0.00           C+0
HETATM   15  C   UNK     0       3.301   1.152  -0.570  0.00  0.00           C+0
HETATM   16  O   UNK     0       3.419   2.182   0.372  0.00  0.00           O+0
HETATM   17  C   UNK     0       1.879  -0.838  -1.122  0.00  0.00           C+0
HETATM   18  O   UNK     0       2.271  -2.021  -0.533  0.00  0.00           O+0
HETATM   19  C   UNK     0       0.358  -0.783  -1.204  0.00  0.00           C+0
HETATM   20  O   UNK     0      -0.214  -2.018  -1.384  0.00  0.00           O+0
HETATM   21  H   UNK     0      -0.553  -3.109   1.148  0.00  0.00           H+0
HETATM   22  H   UNK     0      -4.238  -0.335   1.642  0.00  0.00           H+0
HETATM   23  H   UNK     0      -3.070   2.950  -0.629  0.00  0.00           H+0
HETATM   24  H   UNK     0       0.567  -0.683   0.909  0.00  0.00           H+0
HETATM   25  H   UNK     0       2.328  -0.131   0.893  0.00  0.00           H+0
HETATM   26  H   UNK     0       4.256   0.602  -0.563  0.00  0.00           H+0
HETATM   27  H   UNK     0       3.059   1.626  -1.526  0.00  0.00           H+0
HETATM   28  H   UNK     0       4.253   2.100   0.905  0.00  0.00           H+0
HETATM   29  H   UNK     0       2.350  -0.636  -2.089  0.00  0.00           H+0
HETATM   30  H   UNK     0       2.766  -1.869   0.321  0.00  0.00           H+0
HETATM   31  H   UNK     0       0.110  -0.076  -2.046  0.00  0.00           H+0
HETATM   32  H   UNK     0       0.399  -2.588  -1.944  0.00  0.00           H+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2   21                                                       
CONECT    4    2    5   11                                                  
CONECT    5    4    6   22                                                  
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9   23                                                  
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12    4                                                  
CONECT   12   11   13   19   24                                             
CONECT   13   12   14                                                       
CONECT   14   13   15   17   25                                             
CONECT   15   14   16   26   27                                             
CONECT   16   15   28                                                       
CONECT   17   14   18   19   29                                             
CONECT   18   17   30                                                       
CONECT   19   17   20   12   31                                             
CONECT   20   19   32                                                       
CONECT   21    3                                                            
CONECT   22    5                                                            
CONECT   23    8                                                            
CONECT   24   12                                                            
CONECT   25   14                                                            
CONECT   26   15                                                            
CONECT   27   15                                                            
CONECT   28   16                                                            
CONECT   29   17                                                            
CONECT   30   18                                                            
CONECT   31   19                                                            
CONECT   32   20                                                            
MASTER        0    0    0    0    0    0    0    0   32    0   66    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

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 Mass

288.2109 Da

Monoisotopic Mass

288.05937 Da

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

[H]OC(=O)C1=C([H])C(=O)N([H])C(=O)N1[C@]1([H])O[C@]([H])(C([H])([H])O[H])[C@@]([H])(O[H])[C@@]1([H])O[H]

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

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, simulated)	V.dorna83			2021-09-03	View Spectrum
2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 600 MHz, H₂O, experimental)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, simulated)	varshavi.d26@gmail.com	Not Available	Not Available	2021-08-08	View Spectrum

Species

Species of Origin

Species Name	Source	Reference
Anas platyrhynchos	FooDB	FooDB
Anatidae	FooDB	FooDB
Anser anser	FooDB	FooDB
Bison bison	FooDB	FooDB
Bos taurus	FooDB	FooDB
Bos taurus X Bison bison	FooDB	FooDB
Bubalus bubalis	FooDB	FooDB
Capra aegagrus hircus	FooDB	FooDB
Cervidae	FooDB	FooDB
Cervus canadensis	FooDB	FooDB
Columba	FooDB	FooDB
Columbidae	FooDB	FooDB
Dromaius novaehollandiae	FooDB	FooDB
Equus caballus	FooDB	FooDB
Gallus gallus	FooDB	FooDB
Lagopus muta	FooDB	FooDB
Leporidae	FooDB	FooDB
Lepus timidus	FooDB	FooDB
Melanitta fusca	FooDB	FooDB
Meleagris gallopavo	FooDB	FooDB
Numida meleagris	FooDB	FooDB
Odocoileus	FooDB	FooDB
Oryctolagus	FooDB	FooDB
Ovis aries	FooDB	FooDB
Phaseolus vulgaris	KNApSAcK Database	22123792
Phasianidae	FooDB	FooDB
Phasianus colchicus	FooDB	FooDB
Struthio camelus	FooDB	FooDB
Sus scrofa	FooDB	FooDB
Sus scrofa domestica	FooDB	FooDB

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 )

Physical Properties

State

Solid

Experimental Properties

Property	Value	Reference
Melting Point	> 400 °C	https://en.wikipedia.org/wiki/Orotidine
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

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

External Links

HMDB ID

HMDB0000788

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB 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

Good Scents ID

Not Available

References

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 ]
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. Epub 2004 Sep 16. [PubMed:15375016 ]
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 ]
Matsuo Y, Nishino K, Mizuno K, Akihiro T, Toda T, Matsuo Y, Kaino T, Kawamukai M: Polypeptone induces dramatic cell lysis in ura4 deletion mutants of fission yeast. PLoS One. 2013;8(3):e59887. doi: 10.1371/journal.pone.0059887. Epub 2013 Mar 21. [PubMed:23555823 ]

Showing NP-Card for Orotidine (NP0000088)

MOL for NP0000088 (Orotidine)

3D MOL for NP0000088 (Orotidine)

3D SDF for NP0000088 (Orotidine)

3D-SDF for NP0000088 (Orotidine)

PDB for NP0000088 (Orotidine)

3D PDB for NP0000088 (Orotidine)

SMILES for NP0000088 (Orotidine)

INCHI for NP0000088 (Orotidine)

Structure for NP0000088 (Orotidine)

3D Structure for NP0000088 (Orotidine)