Showing metabocard for 4,5-Dihydroorotic acid (MMDBc0000352)

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Record Information
Version1.0
StatusDetected and Quantified
Creation Date2020-12-10 18:35:56 UTC
Update Date2024-04-30 19:31:54 UTC
Metabolite IDMMDBc0000352
Metabolite Identification
Common Name4,5-Dihydroorotic acid
Description4,5-Dihydroorotic acid, also known as dihydroorotate or hydroorotate is a pyrimidinemonocarboxylic acid that results from the base-catalysed cyclisation of N-alpha-carbethoxyasparagine. It is classified as a secondary amide, a monocarboxylic acid, a pyrimidinemonocarboxylic acid and a N-acylurea. 4,5-Dihydroorotic acid is a derivative of orotic acid which serves as an intermediate in pyrimidine biosynthesis. 4,5-Dihydroorotic acid exists in all living species, ranging from bacteria to plants to humans. 4,5-Dihydroorotic acid is synthesized by the enzyme known as Dihydroorotase (EC 3.5.2.3) which converts carbamoyl aspartic acid into 4,5-dihydroorotic acid as part of the de novo pyrimidine biosynthesis pathway (PMID: 13163076 ). 4,5-Dihydroorotic acid is also a substrate for the enzyme known as dihydroorotate dehydrogenase (DHODH). In mammalian species, DHODH catalyzes the fourth step in the de novo pyrimidine biosynthesis pathway, which involves the ubiquinone-mediated oxidation of dihydroorotate to orotate and the reduction of flavin mononucleotide (FMN) to dihydroflavin mononucleotide (FMNH2). Inhibition of DHODH activity with teriflunomide (an immunomodulatory drug) or expression with RNA interference results in reduced ROS generation and consequent apoptosis of transformed skin and prostate epithelial cells. Mutations in the DHOD gene have been shown to cause Miller syndrome, also known as Genee-Wiedemann syndrome, Wildervanck-Smith syndrome or post-axial acrofacial dystosis (PMID: 19915526 ).
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x000056230827c5f0>

4,5-Dihydroorotic acid.mol
  Mrv1652305261923592D          

 11 11  0  0  0  0            999 V2000
    0.0087    1.0325    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0058    0.2075    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7188   -0.2075    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7159   -1.0325    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.4475    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.4425    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7130   -1.0275    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -1.4374    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7101   -0.2025    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7043    1.4475    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7247    1.4425    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  4  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
  2  9  1  0  0  0  0
  1 10  2  0  0  0  0
  1 11  1  0  0  0  0
M  END
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3D MOL for #<Metabolite:0x000056230827c5f0>

HMDB0000528
     RDKit          3D
4,5-Dihydroorotic acid
 17 17  0  0  0  0  0  0  0  0999 V2000
   -2.0113   -0.2867    1.9855 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4108   -0.1526    0.8840 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2690   -1.0434    0.6053 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6480   -0.5257   -0.4632 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8322    0.1305    0.1090 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1344    1.2775   -0.2512 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5883   -0.5428    1.0389 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0384    0.3591   -1.3895 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1352    1.1177   -1.1849 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4905    1.9949   -2.0265 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8789    0.8455   -0.0049 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.3090   -1.2239    1.5549 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6844   -2.0337    0.3211 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9877   -1.4247   -1.0632 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5879   -0.3425    2.0377 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4963    0.4773   -2.3402 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7421    1.3736    0.1873 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  0
  7 15  1  0
  8 16  1  0
 11 17  1  0
M  END
Download

3D SDF for #<Metabolite:0x000056230827c5f0>

4,5-Dihydroorotic acid.mol
  Mrv1652305261923592D          

 11 11  0  0  0  0            999 V2000
    0.0087    1.0325    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0058    0.2075    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7188   -0.2075    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7159   -1.0325    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.4475    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.4425    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7130   -1.0275    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -1.4374    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7101   -0.2025    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7043    1.4475    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7247    1.4425    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  4  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
  2  9  1  0  0  0  0
  1 10  2  0  0  0  0
  1 11  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0000352

> <DATABASE_NAME>
MIME

> <SMILES>
OC(=O)C1CC(=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)

> <INCHI_KEY>
UFIVEPVSAGBUSI-UHFFFAOYSA-N

> <FORMULA>
C5H6N2O4

> <MOLECULAR_WEIGHT>
158.1121

> <EXACT_MASS>
158.03275669

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
17

> <JCHEM_AVERAGE_POLARIZABILITY>
13.091120354543254

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
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>
95.50000000000001

> <JCHEM_REFRACTIVITY>
31.575400000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.27e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
dihydroorotic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for #<Metabolite:0x000056230827c5f0>

HMDB0000528
     RDKit          3D
4,5-Dihydroorotic acid
 17 17  0  0  0  0  0  0  0  0999 V2000
   -2.0113   -0.2867    1.9855 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4108   -0.1526    0.8840 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2690   -1.0434    0.6053 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6480   -0.5257   -0.4632 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8322    0.1305    0.1090 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1344    1.2775   -0.2512 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5883   -0.5428    1.0389 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0384    0.3591   -1.3895 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1352    1.1177   -1.1849 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4905    1.9949   -2.0265 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8789    0.8455   -0.0049 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.3090   -1.2239    1.5549 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6844   -2.0337    0.3211 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9877   -1.4247   -1.0632 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5879   -0.3425    2.0377 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4963    0.4773   -2.3402 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7421    1.3736    0.1873 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  0
  7 15  1  0
  8 16  1  0
 11 17  1  0
M  END
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PDB for #<Metabolite:0x000056230827c5f0>

HEADER    PROTEIN                                 26-MAY-19   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 4,5-Dihydroorotic acid.mol                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   26-MAY-19         0                                  
HETATM    1  C   UNK     0       0.016   1.927   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.011   0.387   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0       1.342  -0.387   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0       1.336  -1.927   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       2.667  -2.702   0.000  0.00  0.00           O+0
HETATM    6  N   UNK     0       0.000  -2.693   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0      -1.331  -1.918   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -2.667  -2.683   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      -1.326  -0.378   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -1.315   2.702   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       1.353   2.693   0.000  0.00  0.00           O+0
CONECT    1    2   10   11                                                  
CONECT    2    1    3    9                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7    2                                                       
CONECT   10    1                                                            
CONECT   11    1                                                            
MASTER        0    0    0    0    0    0    0    0   11    0   22    0
END
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3D PDB for #<Metabolite:0x000056230827c5f0>

COMPND    HMDB0000528
HETATM    1  O1  UNL     1      -2.011  -0.287   1.985  1.00  0.00           O  
HETATM    2  C1  UNL     1      -1.411  -0.153   0.884  1.00  0.00           C  
HETATM    3  C2  UNL     1      -0.269  -1.043   0.605  1.00  0.00           C  
HETATM    4  C3  UNL     1       0.648  -0.526  -0.463  1.00  0.00           C  
HETATM    5  C4  UNL     1       1.832   0.131   0.109  1.00  0.00           C  
HETATM    6  O2  UNL     1       2.134   1.277  -0.251  1.00  0.00           O  
HETATM    7  O3  UNL     1       2.588  -0.543   1.039  1.00  0.00           O  
HETATM    8  N1  UNL     1       0.038   0.359  -1.390  1.00  0.00           N  
HETATM    9  C5  UNL     1      -1.135   1.118  -1.185  1.00  0.00           C  
HETATM   10  O4  UNL     1      -1.490   1.995  -2.027  1.00  0.00           O  
HETATM   11  N2  UNL     1      -1.879   0.846  -0.005  1.00  0.00           N  
HETATM   12  H1  UNL     1       0.309  -1.224   1.555  1.00  0.00           H  
HETATM   13  H2  UNL     1      -0.684  -2.034   0.321  1.00  0.00           H  
HETATM   14  H3  UNL     1       0.988  -1.425  -1.063  1.00  0.00           H  
HETATM   15  H4  UNL     1       2.588  -0.343   2.038  1.00  0.00           H  
HETATM   16  H5  UNL     1       0.496   0.477  -2.340  1.00  0.00           H  
HETATM   17  H6  UNL     1      -2.742   1.374   0.187  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:0x000056230827c5f0>

OC(=O)C1CC(=O)NC(=O)N1
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INCHI for #<Metabolite:0x000056230827c5f0>

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)
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Synonyms
Molecular FormulaC5H6N2O4
Average Mass158.1121
Monoisotopic Mass158.03275669
IUPAC Name2,6-dioxo-1,3-diazinane-4-carboxylic acid
Traditional Namedihydroorotic acid
CAS Registry NumberNot Available
SMILES
OC(=O)C1CC(=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)
InChI KeyUFIVEPVSAGBUSI-UHFFFAOYSA-N