Showing metabocard for barbiturate (MMDBc0054354)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2022-06-05 23:08:26 UTC
Update Date2024-10-09 15:46:08 UTC
Metabolite IDMMDBc0054354
Metabolite Identification
Common Namebarbiturate
DescriptionBarbituric acid, also known as barbitursaeure or malonylurea, 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. Barbituric acid exists in all living organisms, ranging from bacteria to humans. Barbituric acid is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. Based on a literature review a significant number of articles have been published on Barbituric acid.
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007fdb505835f8>


  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 #<Metabolite:0x00007fdb505835f8>

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 #<Metabolite:0x00007fdb505835f8>


  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>
MMDBc0054354

> <DATABASE_NAME>
MIME

> <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 #<Metabolite:0x00007fdb505835f8>

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 #<Metabolite:0x00007fdb505835f8>

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 #<Metabolite:0x00007fdb505835f8>

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 #<Metabolite:0x00007fdb505835f8>

OC1=NC(=O)N=C(O)C1
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INCHI for #<Metabolite:0x00007fdb505835f8>

InChI=1S/C4H4N2O3/c7-2-1-3(8)6-4(9)5-2/h1H2,(H2,5,6,7,8,9)
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Synonyms
ValueSource
2,4,6(1H,3H,5H)-PyrimidinetrioneChEBI
BarbitursaeureChEBI
MalonylharnstoffChEBI
MalonylureaChEBI
BarbitateGenerator
Barbitic acidGenerator
2,4,6(1H,3H,5H)-Pyrimidinetrione (acd/name 4.0)HMDB
2,4,6-(1H,3H,5H)-PyrimidinetrioneHMDB
2,4,6-PyrimidinetriolHMDB
2,4,6-Pyrimidinetrione(1H,3H,5H)HMDB
2,4,6-TrihydroxypyrimidineHMDB
2,4,6-TrioxohexahydropyrimidineHMDB
6-HydroxyuracilHMDB
BarbiturateHMDB
BarbitursaureHMDB
N,N'-(1,3-dioxo-1,3-propanediyl)-ureaHMDB
NN'-(1,3-Dioxo-1,3-propanediyl)-ureaHMDB
Pyrimidine-2,4,6(1H,3H,5H)-trioneHMDB
PyrimidinetrioneHMDB
Barbituric acid, monosodium saltHMDB
Sodium barbiturateHMDB
Molecular FormulaC4H4N2O3
Average Mass128.0862
Monoisotopic Mass128.022192004
IUPAC Name4,6-dihydroxy-2,5-dihydropyrimidin-2-one
Traditional Namebarbituric acid
CAS Registry NumberNot Available
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