Showing metabocard for L-Dihydroorotic acid (MMDBc0032976)

Plant
Record Information
Version1.0
StatusDetected and Quantified
Creation Date2021-11-19 04:29:38 UTC
Update Date2022-08-31 21:54:46 UTC
Metabolite IDMMDBc0032976
Metabolite Identification
Common NameL-Dihydroorotic acid
DescriptionL-Dihydroorotic acid, also known as (S)-4,5-dihydroorotate or dihydro-L-orotate, belongs to the class of organic compounds known as alpha amino acids and derivatives. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon), or a derivative thereof. L-Dihydroorotic acid is an extremely weak basic (essentially neutral) compound (based on its pKa). The (S)-enantiomer of dihydroorotic acid that is an intermediate in the metabolism of pyridine. L-Dihydroorotic acid exists in all living species, ranging from bacteria to humans. Within humans, L-dihydroorotic acid participates in a number of enzymatic reactions. In particular, L-dihydroorotic acid can be biosynthesized from ureidosuccinic acid through the action of the enzyme cad protein. In addition, L-dihydroorotic acid and quinone can be converted into orotic acid through the action of the enzyme dihydroorotate dehydrogenase (quinone), mitochondrial. In humans, L-dihydroorotic acid is involved in pyrimidine metabolism. Outside of the human body, L-Dihydroorotic acid has been detected, but not quantified in, several different foods, such as american pokeweeds, prunus (cherry, plum), red huckleberries, white lupines, and shallots. This could make L-dihydroorotic acid a potential biomarker for the consumption of these foods.
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x0000560be0459cb8>


  Mrv1652309042000292D          

 11 11  0  0  1  0            999 V2000
    2.8579    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  4  2  1  6  0  0  0
  4  5  1  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
  4 11  1  0  0  0  0
M  END
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3D MOL for #<Metabolite:0x0000560be0459cb8>

HMDB0003349
     RDKit          3D
L-Dihydroorotic acid
 17 17  0  0  0  0  0  0  0  0999 V2000
   -2.6098   -0.6879    1.5485 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7442   -0.3138    0.7103 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5443   -1.1305    0.3609 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5806   -0.0971    0.1672 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.9006   -0.7090    0.1085 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1712   -1.8674   -0.0305 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9722    0.2145    0.2550 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1530    0.5752   -1.0756 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0039    1.4080   -0.8477 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1595    2.5124   -1.4661 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9592    0.9313    0.0847 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7340   -1.5668   -0.6642 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2934   -1.8951    1.0593 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5303    0.5551    1.0130 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9115   -0.0350    0.4313 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5929    0.5255   -1.9781 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7642    1.5805    0.3234 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  2  0
  5  7  1  0
  4  8  1  0
  8  9  1  0
  9 10  2  0
  9 11  1  0
 11  2  1  0
  3 12  1  0
  3 13  1  0
  4 14  1  1
  7 15  1  0
  8 16  1  0
 11 17  1  0
M  END
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3D SDF for #<Metabolite:0x0000560be0459cb8>


  Mrv1652309042000292D          

 11 11  0  0  1  0            999 V2000
    2.8579    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  4  2  1  6  0  0  0
  4  5  1  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
  4 11  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0032976

> <DATABASE_NAME>
MIME

> <SMILES>
OC(=O)[C@@H]1CC(=O)NC(=O)N1

> <INCHI_IDENTIFIER>
InChI=1S/C5H6N2O4/c8-3-1-2(4(9)10)6-5(11)7-3/h2H,1H2,(H,9,10)(H2,6,7,8,11)/t2-/m0/s1

> <INCHI_KEY>
UFIVEPVSAGBUSI-REOHCLBHSA-N

> <FORMULA>
C5H6N2O4

> <MOLECULAR_WEIGHT>
158.1121

> <EXACT_MASS>
158.03275669

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
17

> <JCHEM_AVERAGE_POLARIZABILITY>
12.955416264529363

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(4S)-2,6-dioxo-1,3-diazinane-4-carboxylic acid

> <ALOGPS_LOGP>
-1.70

> <JCHEM_LOGP>
-1.5232681353333333

> <ALOGPS_LOGS>
-1.10

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
11.713668138573995

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.2849203199118633

> <JCHEM_PKA_STRONGEST_BASIC>
-8.186843445720307

> <JCHEM_POLAR_SURFACE_AREA>
95.5

> <JCHEM_REFRACTIVITY>
31.575400000000005

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.27e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
L-dihydroorotic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x0000560be0459cb8>

HMDB0003349
     RDKit          3D
L-Dihydroorotic acid
 17 17  0  0  0  0  0  0  0  0999 V2000
   -2.6098   -0.6879    1.5485 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7442   -0.3138    0.7103 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5443   -1.1305    0.3609 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5806   -0.0971    0.1672 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.9006   -0.7090    0.1085 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1712   -1.8674   -0.0305 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9722    0.2145    0.2550 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1530    0.5752   -1.0756 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0039    1.4080   -0.8477 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1595    2.5124   -1.4661 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9592    0.9313    0.0847 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7340   -1.5668   -0.6642 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2934   -1.8951    1.0593 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5303    0.5551    1.0130 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9115   -0.0350    0.4313 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5929    0.5255   -1.9781 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7642    1.5805    0.3234 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  2  0
  5  7  1  0
  4  8  1  0
  8  9  1  0
  9 10  2  0
  9 11  1  0
 11  2  1  0
  3 12  1  0
  3 13  1  0
  4 14  1  1
  7 15  1  0
  8 16  1  0
 11 17  1  0
M  END
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PDB for #<Metabolite:0x0000560be0459cb8>

HEADER    PROTEIN                                 04-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-20         0                                  
HETATM    1  O   UNK     0       5.335   0.000   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       4.001  -2.310   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      -1.334  -0.770   0.000  0.00  0.00           O+0
HETATM    8  N   UNK     0       0.000   1.540   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       1.334   3.850   0.000  0.00  0.00           O+0
HETATM   11  N   UNK     0       2.667   1.540   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5   11                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9                                                       
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9    4                                                       
MASTER        0    0    0    0    0    0    0    0   11    0   22    0
END
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3D PDB for #<Metabolite:0x0000560be0459cb8>

COMPND    HMDB0003349
HETATM    1  O1  UNL     1      -2.610  -0.688   1.549  1.00  0.00           O  
HETATM    2  C1  UNL     1      -1.744  -0.314   0.710  1.00  0.00           C  
HETATM    3  C2  UNL     1      -0.544  -1.130   0.361  1.00  0.00           C  
HETATM    4  C3  UNL     1       0.581  -0.097   0.167  1.00  0.00           C  
HETATM    5  C4  UNL     1       1.901  -0.709   0.108  1.00  0.00           C  
HETATM    6  O2  UNL     1       2.171  -1.867  -0.031  1.00  0.00           O  
HETATM    7  O3  UNL     1       2.972   0.215   0.255  1.00  0.00           O  
HETATM    8  N1  UNL     1       0.153   0.575  -1.076  1.00  0.00           N  
HETATM    9  C5  UNL     1      -1.004   1.408  -0.848  1.00  0.00           C  
HETATM   10  O4  UNL     1      -1.159   2.512  -1.466  1.00  0.00           O  
HETATM   11  N2  UNL     1      -1.959   0.931   0.085  1.00  0.00           N  
HETATM   12  H1  UNL     1      -0.734  -1.567  -0.664  1.00  0.00           H  
HETATM   13  H2  UNL     1      -0.293  -1.895   1.059  1.00  0.00           H  
HETATM   14  H3  UNL     1       0.530   0.555   1.013  1.00  0.00           H  
HETATM   15  H4  UNL     1       3.912  -0.035   0.431  1.00  0.00           H  
HETATM   16  H5  UNL     1       0.593   0.525  -1.978  1.00  0.00           H  
HETATM   17  H6  UNL     1      -2.764   1.581   0.323  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3   11
CONECT    3    4   12   13
CONECT    4    5    8   14
CONECT    5    6    6    7
CONECT    7   15
CONECT    8    9   16
CONECT    9   10   10   11
CONECT   11   17
END
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SMILES for #<Metabolite:0x0000560be0459cb8>

OC(=O)[C@@H]1CC(=O)NC(=O)N1
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INCHI for #<Metabolite:0x0000560be0459cb8>

InChI=1S/C5H6N2O4/c8-3-1-2(4(9)10)6-5(11)7-3/h2H,1H2,(H,9,10)(H2,6,7,8,11)/t2-/m0/s1
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Synonyms
ValueSource
(S)-4,5-Dihydroorotic acidChEBI
Dihydro-L-orotic acidChEBI
(S)-4,5-DihydroorotateKegg
L-DihydroorotateKegg
Dihydro-L-orotateGenerator
(S)-DihydroorotateHMDB
4,5-Dihydroorotic acid, (L)-isomerHMDB
5,6-DihydroorotateHMDB
4,5-Dihydroorotic acidHMDB
4,5-Dihydroorotic acid, (DL)-isomerHMDB
DihydroorotateHMDB
Hydroorotic acidHMDB
4,5-Dihydroorotic acid, (D)-isomerHMDB
Molecular FormulaC5H6N2O4
Average Mass158.1121
Monoisotopic Mass158.03275669
IUPAC Name(4S)-2,6-dioxo-1,3-diazinane-4-carboxylic acid
Traditional NameL-dihydroorotic acid
CAS Registry Number5988-19-2
SMILES
OC(=O)[C@@H]1CC(=O)NC(=O)N1
InChI Identifier
InChI=1S/C5H6N2O4/c8-3-1-2(4(9)10)6-5(11)7-3/h2H,1H2,(H,9,10)(H2,6,7,8,11)/t2-/m0/s1
InChI KeyUFIVEPVSAGBUSI-REOHCLBHSA-N