Showing metabocard for barbiturate (MMDBc0054354)

Xenobiotic
Record Information
Version2.0
StatusDetected and Quantified
Creation Date2022-06-05 23:08:26 UTC
Update Date2025-10-07 16:08:28 UTC
Metabolite IDMMDBc0054354
Metabolite Identification
Common Namebarbiturate
DescriptionBarbiturate is a class of organic compounds known for their sedative and anticonvulsant properties, belonging to the chemical class of barbiturates. These compounds typically feature a barbituric acid core structure, characterized by a pyrimidine ring with various substituents that influence their pharmacological effects. The chemistry of barbiturates involves their metabolism primarily through hepatic pathways, where they interact with enzymes such as cytochrome P450, leading to their biotransformation and elimination. Biologically, barbiturates can modulate neurotransmitter systems, particularly enhancing the effects of gamma-aminobutyric acid (GABA), which plays a crucial role in inhibitory signaling in the central nervous system. For instance, Primidone, a barbiturate anticonvulsant, is initiated for therapeutic purposes in managing seizures (PMID:41019829 ). Additionally, certain barbiturate derivatives have shown potent effects on glioblastoma cell viability, indicating their potential in cancer research (PMID:40994189 ). The constitutive androstane receptor (CAR) has been identified as a nuclear receptor for various xenobiotics, including barbiturates, highlighting their interaction with biological pathways (PMID:40947077 ). Furthermore, barbiturates have been associated with increased opioid use in migraine management (PMID:40971111 ).
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f9aa33f9338>


  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:0x00007f9aa33f9338>

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:0x00007f9aa33f9338>


  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:0x00007f9aa33f9338>

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:0x00007f9aa33f9338>

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:0x00007f9aa33f9338>

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:0x00007f9aa33f9338>

OC1=NC(=O)N=C(O)C1
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INCHI for #<Metabolite:0x00007f9aa33f9338>

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