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Showing metabocard for Barbituric acid (HMDB0041833)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-13 11:41:46 UTC
Update Date2023-02-21 17:28:59 UTC
HMDB IDHMDB0041833
Secondary Accession Numbers
  • HMDB41833
Metabolite Identification
Common NameBarbituric acid
DescriptionBarbituric acid or malonylurea or 6-hydroxyuracil is an organic compound based on a pyrimidine heterocyclic skeleton. It is an odorless powder soluble in water. Barbituric acid is the parent compound of barbiturate drugs, although barbituric acid itself is not pharmacologically active. The compound was discovered by the German chemist Adolf von Baeyer on December 4, 1864, the feast of Saint Barbara (who gave the compound its namesake), by combining urea and malonic acid in a condensation reaction. Malonic acid has since been replaced by diethyl malonate, as using the ester avoids the problem of having to deal with the acidity of the carboxylic acid and its unreactive carboxylate.
Structure
Data?1677000539
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0041833 (Barbituric acid)

  Mrv0541 09041212432D          

  9  9  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
    0.7145    1.2375    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
    0.0000    0.0000    0.0000 C   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   -0.4125    0.0000 N   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 O   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
  2  1  1  0  0  0  0
  3  1  1  0  0  0  0
  5  2  2  0  0  0  0
  5  4  1  0  0  0  0
  6  3  2  0  0  0  0
  6  4  1  0  0  0  0
  7  2  1  0  0  0  0
  8  3  1  0  0  0  0
  9  4  2  0  0  0  0
M  END
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3D MOL for HMDB0041833 (Barbituric acid)

HMDB0041833
     RDKit          3D
Barbituric acid
 13 13  0  0  0  0  0  0  0  0999 V2000
   -1.6074    2.4626    1.3231 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9821    1.5126    0.7552 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6335    0.3926    0.2045 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0100   -0.5616   -0.3655 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7826   -1.6483   -0.8878 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4504   -0.5938   -0.5079 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0801    0.5876    0.0779 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4946    0.6978    0.0166 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4270    1.5309    0.6445 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0341   -2.4185   -0.2712 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8934   -1.5456   -0.1198 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7364   -0.5713   -1.6109 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9677    0.1549    0.7412 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  4  6  1  0
  6  7  1  0
  7  8  1  0
  7  9  2  0
  9  2  1  0
  5 10  1  0
  6 11  1  0
  6 12  1  0
  8 13  1  0
M  END
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3D SDF for HMDB0041833 (Barbituric acid)

  Mrv0541 09041212432D          

  9  9  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
    0.7145    1.2375    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
    0.0000    0.0000    0.0000 C   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   -0.4125    0.0000 N   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 O   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
  2  1  1  0  0  0  0
  3  1  1  0  0  0  0
  5  2  2  0  0  0  0
  5  4  1  0  0  0  0
  6  3  2  0  0  0  0
  6  4  1  0  0  0  0
  7  2  1  0  0  0  0
  8  3  1  0  0  0  0
  9  4  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0041833

> <DATABASE_NAME>
hmdb

> <SMILES>
OC1=NC(=O)N=C(O)C1

> <INCHI_IDENTIFIER>
InChI=1S/C4H4N2O3/c7-2-1-3(8)6-4(9)5-2/h1H2,(H2,5,6,7,8,9)

> <INCHI_KEY>
HNYOPLTXPVRDBG-UHFFFAOYSA-N

> <FORMULA>
C4H4N2O3

> <MOLECULAR_WEIGHT>
128.0862

> <EXACT_MASS>
128.022192004

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
10.275841688572246

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
4,6-dihydroxy-2,5-dihydropyrimidin-2-one

> <ALOGPS_LOGP>
-0.61

> <JCHEM_LOGP>
-0.5360414813333334

> <ALOGPS_LOGS>
-1.50

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.84604724695843

> <JCHEM_PKA_STRONGEST_ACIDIC>
5.451664866139199

> <JCHEM_PKA_STRONGEST_BASIC>
-4.488599264263565

> <JCHEM_POLAR_SURFACE_AREA>
82.25

> <JCHEM_REFRACTIVITY>
26.618199999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.04e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
barbituric acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0041833 (Barbituric acid)

HMDB0041833
     RDKit          3D
Barbituric acid
 13 13  0  0  0  0  0  0  0  0999 V2000
   -1.6074    2.4626    1.3231 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9821    1.5126    0.7552 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6335    0.3926    0.2045 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0100   -0.5616   -0.3655 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7826   -1.6483   -0.8878 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4504   -0.5938   -0.5079 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0801    0.5876    0.0779 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4946    0.6978    0.0166 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4270    1.5309    0.6445 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0341   -2.4185   -0.2712 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8934   -1.5456   -0.1198 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7364   -0.5713   -1.6109 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9677    0.1549    0.7412 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  4  6  1  0
  6  7  1  0
  7  8  1  0
  7  9  2  0
  9  2  1  0
  5 10  1  0
  6 11  1  0
  6 12  1  0
  8 13  1  0
M  END
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PDB for HMDB0041833 (Barbituric acid)

HEADER    PROTEIN                                 04-SEP-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-12         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM    6  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM    7  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
CONECT    1    2    3                                                       
CONECT    2    1    5    7                                                  
CONECT    3    1    6    8                                                  
CONECT    4    5    6    9                                                  
CONECT    5    2    4                                                       
CONECT    6    3    4                                                       
CONECT    7    2                                                            
CONECT    8    3                                                            
CONECT    9    4                                                            
MASTER        0    0    0    0    0    0    0    0    9    0   18    0
END
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3D PDB for HMDB0041833 (Barbituric acid)

COMPND    HMDB0041833
HETATM    1  O1  UNL     1      -1.607   2.463   1.323  1.00  0.00           O  
HETATM    2  C1  UNL     1      -0.982   1.513   0.755  1.00  0.00           C  
HETATM    3  N1  UNL     1      -1.633   0.393   0.205  1.00  0.00           N  
HETATM    4  C2  UNL     1      -1.010  -0.562  -0.365  1.00  0.00           C  
HETATM    5  O2  UNL     1      -1.783  -1.648  -0.888  1.00  0.00           O  
HETATM    6  C3  UNL     1       0.450  -0.594  -0.508  1.00  0.00           C  
HETATM    7  C4  UNL     1       1.080   0.588   0.078  1.00  0.00           C  
HETATM    8  O3  UNL     1       2.495   0.698   0.017  1.00  0.00           O  
HETATM    9  N2  UNL     1       0.427   1.531   0.645  1.00  0.00           N  
HETATM   10  H1  UNL     1      -2.034  -2.418  -0.271  1.00  0.00           H  
HETATM   11  H2  UNL     1       0.893  -1.546  -0.120  1.00  0.00           H  
HETATM   12  H3  UNL     1       0.736  -0.571  -1.611  1.00  0.00           H  
HETATM   13  H4  UNL     1       2.968   0.155   0.741  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    9
CONECT    3    4    4
CONECT    4    5    6
CONECT    5   10
CONECT    6    7   11   12
CONECT    7    8    9    9
CONECT    8   13
END
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SMILES for HMDB0041833 (Barbituric acid)

OC1=NC(=O)N=C(O)C1
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INCHI for HMDB0041833 (Barbituric acid)

InChI=1S/C4H4N2O3/c7-2-1-3(8)6-4(9)5-2/h1H2,(H2,5,6,7,8,9)
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
Chemical FormulaC4H4N2O3
Average Molecular Weight128.0862
Monoisotopic Molecular Weight128.022192004
IUPAC Name4,6-dihydroxy-2,5-dihydropyrimidin-2-one
Traditional Namebarbituric acid
CAS Registry Number67-52-7
SMILES
OC1=NC(=O)N=C(O)C1
InChI Identifier
InChI=1S/C4H4N2O3/c7-2-1-3(8)6-4(9)5-2/h1H2,(H2,5,6,7,8,9)
InChI KeyHNYOPLTXPVRDBG-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as pyrimidones. Pyrimidones are compounds that contain a pyrimidine ring, which bears a ketone. Pyrimidine is a 6-membered ring consisting of four carbon atoms and two nitrogen centers at the 1- and 3- ring positions.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassDiazines
Sub ClassPyrimidines and pyrimidine derivatives
Direct ParentPyrimidones
Alternative Parents
Substituents
  • Pyrimidone
  • Hydropyrimidine
  • 2,5-dihydropyrimidine
  • Carbonic acid derivative
  • Propargyl-type 1,3-dipolar organic compound
  • Organic 1,3-dipolar compound
  • Azacycle
  • Organic oxide
  • Organooxygen compound
  • Organonitrogen compound
  • Organopnictogen compound
  • Organic oxygen compound
  • Carbonyl group
  • Organic nitrogen compound
  • Hydrocarbon derivative
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Source
ProcessNot Available
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point248 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility1.9e-05 mg/mL at 37 °CNot Available
LogP-1.47Not Available
Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct TypeData SourceCCS Value (Å2)Reference
[M-H]-MetCCS_train_neg112.69230932474
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID5976
KEGG Compound IDC00813
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkBarbituric_acid
METLIN IDNot Available
PubChem Compound6211
PDB IDNot Available
ChEBI ID16294
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