Showing metabocard for orotate (MMDBc0054616)

Microbial
Record Information
Version2.0
StatusDetected and Quantified
Creation Date2022-06-05 23:21:22 UTC
Update Date2025-10-07 16:08:36 UTC
Metabolite IDMMDBc0054616
Metabolite Identification
Common Nameorotate
DescriptionOrotate is a pyrimidine derivative, classified as a metabolite in the realm of biochemistry. Its chemical structure features a six-membered ring containing two nitrogen atoms and a carboxylate group, which plays a crucial role in various biochemical pathways. Orotate is primarily involved in the de novo synthesis of pyrimidines, acting as an intermediate in the conversion of dihydroorotate to orotate through the action of dihydroorotate dehydrogenase (DHODH), a flavoprotein that utilizes FMN as a cofactor (PMID:40914975 ). Variants of DHODH, such as DHOD1B, exhibit altered catalytic properties influenced by orotate binding, affecting electron distribution and hydride transfer rates (PMID:40914975 ). Additionally, orotate phosphoribosyl transferase (URA5) has been studied for its potential to degrade orotate in specific conditions (PMID:40931349 ). Elevated levels of orotate have been observed in certain biological contexts, such as cow milk (PMID:41003006 ) and in conditions of hepatocyte-specific LONP1 deficiency, which leads to increased orotic acid levels (PMID:40784490 ). Furthermore, lithium orotate has been investigated for its neuroprotective effects in Alzheimer's disease models (PMID:40770094 ).
Structure
MOLSDFPDBSMILESInChI

MOL for #<Metabolite:0x00007f2e24e53220>


  Mrv1533004241518432D          

 11 11  0  0  0  0            999 V2000
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 N   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
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
  1  2  2  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
  1  7  1  0  0  0  0
  7  8  2  0  0  0  0
  2  9  1  0  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
M  CHG  1  11  -1
M  END
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3D MOL for #<Metabolite:0x00007f2e24e53220>

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3D SDF for #<Metabolite:0x00007f2e24e53220>

  Mrv1533004241518432D          

 11 11  0  0  0  0            999 V2000
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 N   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
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
  1  2  2  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
  1  7  1  0  0  0  0
  7  8  2  0  0  0  0
  2  9  1  0  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
M  CHG  1  11  -1
M  END
> <DATABASE_ID>
MMDBc0054616

> <DATABASE_NAME>
MIME

> <SMILES>
[O-]C(=O)C1=CC(=O)NC(=O)N1

> <INCHI_IDENTIFIER>
InChI=1S/C5H4N2O4/c8-3-1-2(4(9)10)6-5(11)7-3/h1H,(H,9,10)(H2,6,7,8,11)/p-1

> <INCHI_KEY>
PXQPEWDEAKTCGB-UHFFFAOYSA-M

> <FORMULA>
C5H3N2O4

> <MOLECULAR_WEIGHT>
155.09

> <EXACT_MASS>
155.009830165

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
14

> <JCHEM_AVERAGE_POLARIZABILITY>
12.013279121666386

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
-1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylate

> <ALOGPS_LOGP>
-0.38

> <JCHEM_LOGP>
-1.227664501

> <ALOGPS_LOGS>
-1.04

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
8.781577888084735

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.827266331449678

> <JCHEM_PKA_STRONGEST_BASIC>
-6.031557162374665

> <JCHEM_POLAR_SURFACE_AREA>
98.33000000000001

> <JCHEM_REFRACTIVITY>
44.111700000000006

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.58e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
orotate

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for #<Metabolite:0x00007f2e24e53220>
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PDB for #<Metabolite:0x00007f2e24e53220>
HEADER    PROTEIN                                 24-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-APR-15         0                                  
HETATM    1  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0       1.334  -0.770   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0       0.000  -0.000   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      -1.334  -0.770   0.000  0.00  0.00           O+0
HETATM    6  N   UNK     0       0.000   1.540   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       1.334   3.850   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       5.335  -0.000   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       4.001  -2.310   0.000  0.00  0.00           O-1
CONECT    1    2    7                                                       
CONECT    2    1    3    9                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7                                                       
CONECT    7    6    1    8                                                  
CONECT    8    7                                                            
CONECT    9    2   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9                                                            
MASTER        0    0    0    0    0    0    0    0   11    0   22    0
END

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3D PDB for #<Metabolite:0x00007f2e24e53220>
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SMILES for #<Metabolite:0x00007f2e24e53220>
[O-]C(=O)C1=CC(=O)NC(=O)N1
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INCHI for #<Metabolite:0x00007f2e24e53220>
InChI=1S/C5H4N2O4/c8-3-1-2(4(9)10)6-5(11)7-3/h1H,(H,9,10)(H2,6,7,8,11)/p-1
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Synonyms
ValueSource
Orotic acidGenerator
Molecular FormulaC5H3N2O4
Average Mass155.09
Monoisotopic Mass155.009830165
IUPAC Name2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylate
Traditional Nameorotate
CAS Registry NumberNot Available
SMILES
[O-]C(=O)C1=CC(=O)NC(=O)N1
InChI Identifier
InChI=1S/C5H4N2O4/c8-3-1-2(4(9)10)6-5(11)7-3/h1H,(H,9,10)(H2,6,7,8,11)/p-1
InChI KeyPXQPEWDEAKTCGB-UHFFFAOYSA-M