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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 Malonic acid has since been replaced by diethyl malonate, as using the ester avoids the problem of having to deal with the acidity of the carboxylic acid and its unreactive carboxylate.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
Download

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

$$$$
Download

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
Download

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
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
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
PropertyValueSource
Water Solubility4.04 g/LALOGPS
logP-0.61ALOGPS
logP-0.54ChemAxon
logS-1.5ALOGPS
pKa (Strongest Acidic)5.45ChemAxon
pKa (Strongest Basic)-4.5ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area82.25 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity26.62 m³·mol⁻¹ChemAxon
Polarizability10.28 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+128.10531661259
DarkChem[M-H]-121.92731661259
DeepCCS[M+H]+127.99330932474
DeepCCS[M-H]-125.67130932474
DeepCCS[M-2H]-161.71130932474
DeepCCS[M+Na]+136.630932474
AllCCS[M+H]+126.932859911
AllCCS[M+H-H2O]+122.232859911
AllCCS[M+NH4]+131.432859911
AllCCS[M+Na]+132.632859911
AllCCS[M-H]-119.032859911
AllCCS[M+Na-2H]-121.132859911
AllCCS[M+HCOO]-123.432859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.1.07 minutes32390414
Predicted by Siyang on May 30, 20229.298 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20224.33 minutes32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid114.4 seconds40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid979.6 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid350.7 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid83.9 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid238.6 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid77.6 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid264.4 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid322.6 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)244.5 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid645.3 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid157.0 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid857.4 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid230.5 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid249.7 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate669.9 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA230.5 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water234.8 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
Barbituric acidOC1=NC(=O)N=C(O)C12936.4Standard polar33892256
Barbituric acidOC1=NC(=O)N=C(O)C11475.3Standard non polar33892256
Barbituric acidOC1=NC(=O)N=C(O)C11410.5Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Barbituric acid,1TMS,isomer #1C[Si](C)(C)OC1=NC(=O)N=C(O)C11552.5Semi standard non polar33892256
Barbituric acid,2TMS,isomer #1C[Si](C)(C)OC1=NC(=O)N=C(O[Si](C)(C)C)C11635.2Semi standard non polar33892256
Barbituric acid,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC1=NC(=O)N=C(O)C11721.6Semi standard non polar33892256
Barbituric acid,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC1=NC(=O)N=C(O[Si](C)(C)C(C)(C)C)C11952.4Semi standard non polar33892256
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