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Showing metabocard for L-Dihydroorotic acid (HMDB0003349)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2006-08-12 19:12:38 UTC
Update Date2022-09-22 18:34:17 UTC
HMDB IDHMDB0003349
Secondary Accession Numbers
  • HMDB03349
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. 4,5-Dihydroorotic acid is a derivative of orotic acid which serves as an intermediate in pyrimidine biosynthesis. L-Dihydroorotic acid is a drug. 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; which is catalyzed by 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 the metabolic disorder called the beta-ureidopropionase deficiency pathway. Outside of the human body, L-dihydroorotic acid has been detected, but not quantified in several different foods, such as black chokeberries, vanilla, sweet basils, soy beans, and broad beans.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0003349 (L-Dihydroorotic acid)

  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 HMDB0003349 (L-Dihydroorotic acid)

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 HMDB0003349 (L-Dihydroorotic acid)

  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>
HMDB0003349

> <DATABASE_NAME>
hmdb

> <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 HMDB0003349 (L-Dihydroorotic acid)

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 HMDB0003349 (L-Dihydroorotic acid)

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 HMDB0003349 (L-Dihydroorotic acid)

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 HMDB0003349 (L-Dihydroorotic acid)

OC(=O)[C@@H]1CC(=O)NC(=O)N1
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INCHI for HMDB0003349 (L-Dihydroorotic acid)

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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View in JSmolView NMR AssignmentsView Stereo Labels
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
Chemical FormulaC5H6N2O4
Average Molecular Weight158.1121
Monoisotopic Molecular Weight158.03275669
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
Chemical Taxonomy
Description 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.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct ParentAlpha amino acids and derivatives
Alternative Parents
Substituents
  • Alpha-amino acid or derivatives
  • N-acyl urea
  • Pyrimidone
  • Ureide
  • 1,3-diazinane
  • Pyrimidine
  • Dicarboximide
  • Urea
  • Carbonic acid derivative
  • Azacycle
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Organoheterocyclic compound
  • Hydrocarbon derivative
  • Organic oxide
  • Organooxygen compound
  • Organonitrogen compound
  • Organopnictogen compound
  • Organic oxygen compound
  • Carbonyl group
  • Organic nitrogen compound
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationRoute of exposureSource
Process
Naturally occurring process
Role
Industrial application
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct TypeData SourceCCS Value (Å2)Reference
[M-H]-Astarita_neg123.030932474
[M-H]-Not Available132.4http://allccs.zhulab.cn/database/detail?ID=AllCCS00001767
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm (predicted from logP)
Biospecimen Locations
  • Blood
  • Feces
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedCancer patients undergoing total body irradiation details
UrineDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedCancer patients undergoing total body irradiation details
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDDB02129
Phenol Explorer Compound IDNot Available
FooDB IDFDB023149
KNApSAcK IDC00007302
Chemspider ID388355
KEGG Compound IDC00337
BioCyc IDDI-H-OROTATE
BiGG ID34662
Wikipedia Link4,5-Dihydroorotic acid
METLIN ID6899
PubChem Compound439216
PDB IDNot Available
ChEBI ID17025
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available

Enzymes

Enzyme Details
1. Dihydroorotate dehydrogenase (quinone), mitochondrial
General function:
Involved in catalytic activity
Specific function:
Catalyzes the conversion of dihydroorotate to orotate with quinone as electron acceptor.
Gene Name:
DHODH
Uniprot ID:
Q02127
Molecular weight:
42866.93
Reactions
L-Dihydroorotic acid + a quinone → Orotic acid + a quinoldetails
L-Dihydroorotic acid + Quinone → Orotic acid + Hydroquinonedetails
Enzyme Details
2. CAD protein
General function:
Involved in hydrolase activity
Specific function:
This protein is a "fusion" protein encoding four enzymatic activities of the pyrimidine pathway (GATase, CPSase, ATCase and DHOase).
Gene Name:
CAD
Uniprot ID:
P27708
Molecular weight:
242981.73
Reactions
L-Dihydroorotic acid + Water → Ureidosuccinic aciddetails