Np mrd loader

Showing NP-Card for Barbituric acid (NP0002705)

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Record Information
Version2.0
Created at2020-11-23 19:38:23 UTC
Updated at2021-08-12 19:51:54 UTC
NP-MRD IDNP0002705
Secondary Accession NumbersNone
Natural Product Identification
Common NameBarbituric acid
Provided ByBMRBBMRB logo
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. Barbituric acid was first documented in 1987 (PMID: 3654008). Based on a literature review a small amount of articles have been published on Barbituric acid (PMID: 22139480) (PMID: 23038042) (PMID: 23915243).
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0002705 (Barbituric acid)


     RDKit          2D

 13 13  0  0  0  0  0  0  0  0999 V2000
   -1.3232   -2.5981    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5732   -1.2990    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3232   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5732    1.2990    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3232    2.5981    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9268    1.2990    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6768    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1768    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9268   -1.2990    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4723   -0.9642    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4723    0.9642    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6768    2.5981    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6768   -2.5981    0.0000 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  2  0
  4  6  1  0
  6  7  1  0
  7  8  2  0
  7  9  1  0
  9  2  1  0
  3 10  1  6
  3 11  1  0
  6 12  1  0
  9 13  1  0
M  END
Download

3D MOL for NP0002705 (Barbituric acid)

NP0002705
     RDKit          3D

 13 13  0  0  0  0  0  0  0  0999 V2000
   -1.0253    3.1240    0.0649 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6168    1.9289    0.0868 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5103    0.8272    0.1892 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1255   -0.3885    0.2135 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0542   -1.4456    0.3163 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2850   -0.7753    0.1379 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1907    0.3689    0.0331 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5878    0.1533   -0.0485 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7494    1.5678    0.0131 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3076   -1.8542   -0.5889 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3790   -1.3268   -0.8547 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5759   -1.4879    0.9489 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8719   -0.6918   -0.5115 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 NP0002705 (Barbituric acid)


     RDKit          2D

 13 13  0  0  0  0  0  0  0  0999 V2000
   -1.3232   -2.5981    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5732   -1.2990    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3232   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5732    1.2990    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3232    2.5981    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9268    1.2990    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6768    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1768    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9268   -1.2990    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4723   -0.9642    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4723    0.9642    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6768    2.5981    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6768   -2.5981    0.0000 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  2  0
  4  6  1  0
  6  7  1  0
  7  8  2  0
  7  9  1  0
  9  2  1  0
  3 10  1  6
  3 11  1  0
  6 12  1  0
  9 13  1  0
M  END
> <DATABASE_ID>
NP0002705

> <DATABASE_NAME>
NP-MRD

> <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 NP0002705 (Barbituric acid)

NP0002705
     RDKit          3D

 13 13  0  0  0  0  0  0  0  0999 V2000
   -1.0253    3.1240    0.0649 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6168    1.9289    0.0868 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5103    0.8272    0.1892 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1255   -0.3885    0.2135 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0542   -1.4456    0.3163 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2850   -0.7753    0.1379 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1907    0.3689    0.0331 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5878    0.1533   -0.0485 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7494    1.5678    0.0131 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3076   -1.8542   -0.5889 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3790   -1.3268   -0.8547 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5759   -1.4879    0.9489 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8719   -0.6918   -0.5115 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 NP0002705 (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 NP0002705 (Barbituric acid)

COMPND    NP0002705
HETATM    1  O1  UNL     1      -1.025   3.124   0.065  1.00  0.00           O  
HETATM    2  C1  UNL     1      -0.617   1.929   0.087  1.00  0.00           C  
HETATM    3  N1  UNL     1      -1.510   0.827   0.189  1.00  0.00           N  
HETATM    4  C2  UNL     1      -1.125  -0.388   0.213  1.00  0.00           C  
HETATM    5  O2  UNL     1      -2.054  -1.446   0.316  1.00  0.00           O  
HETATM    6  C3  UNL     1       0.285  -0.775   0.138  1.00  0.00           C  
HETATM    7  C4  UNL     1       1.191   0.369   0.033  1.00  0.00           C  
HETATM    8  O3  UNL     1       2.588   0.153  -0.049  1.00  0.00           O  
HETATM    9  N2  UNL     1       0.749   1.568   0.013  1.00  0.00           N  
HETATM   10  H1  UNL     1      -2.308  -1.854  -0.589  1.00  0.00           H  
HETATM   11  H2  UNL     1       0.379  -1.327  -0.855  1.00  0.00           H  
HETATM   12  H3  UNL     1       0.576  -1.488   0.949  1.00  0.00           H  
HETATM   13  H4  UNL     1       2.872  -0.692  -0.512  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 NP0002705 (Barbituric acid)

OC1=NC(=O)N=C(O)C1
Download

INCHI for NP0002705 (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 JSmol
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 Mass128.0862 Da
Monoisotopic Mass128.02219 Da
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
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of OriginNot Available
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 ParentsNot Available
SubstituentsNot Available
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
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
HMDB IDHMDB0041833
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB 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
Good Scents IDNot Available
References
General References
  1. Azizian H, Nabati F, Sharifi A, Siavoshi F, Mahdavi M, Amanlou M: Large-scale virtual screening for the identification of new Helicobacter pylori urease inhibitor scaffolds. J Mol Model. 2012 Jul;18(7):2917-27. doi: 10.1007/s00894-011-1310-2. Epub 2011 Dec 3. [PubMed:22139480 ]
  2. Sen A, Ganguly B: Is dual morphology of rock-salt crystals possible with a single additive? The answer is yes, with barbituric acid. Angew Chem Int Ed Engl. 2012 Nov 5;51(45):11279-83. doi: 10.1002/anie.201206170. Epub 2012 Oct 4. [PubMed:23038042 ]
  3. Dong A, Sun Y, Lan S, Wang Q, Cai Q, Qi X, Zhang Y, Gao G, Liu F, Harnoode C: Barbituric acid-based magnetic N-halamine nanoparticles as recyclable antibacterial agents. ACS Appl Mater Interfaces. 2013 Aug 28;5(16):8125-33. doi: 10.1021/am402191j. Epub 2013 Aug 16. [PubMed:23915243 ]
  4. Harle DG, Baldo BA, Smal MA, Fisher MM: Drugs as allergens: the molecular basis of IgE binding to thiopentone. Int Arch Allergy Appl Immunol. 1987;84(3):277-83. doi: 10.1159/000234435. [PubMed:3654008 ]