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Showing NP-Card for Parabanic acid (NP0002892)

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Record Information
Version1.0
Created at2020-11-23 19:42:58 UTC
Updated at2021-08-12 19:52:26 UTC
NP-MRD IDNP0002892
Secondary Accession NumbersNone
Natural Product Identification
Common NameParabanic acid
Provided ByBMRBBMRB logo
DescriptionParabanic Acid, also known as parabanate or oxalylurea, belongs to the class of organic compounds known as imidazolinones. These are organic compounds containing an imidazolinone moiety, which is an imidazoline ring bearing a ketone. Parabanic Acid is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. It was first documented in 1954 (PMID: 13215781). Based on a literature review a small amount of articles have been published on Parabanic Acid (PMID: 17984079) (PMID: 2155712) (PMID: 22583701) (PMID: 5453531).
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0002892 (Parabanic acid)


     RDKit          2D

 10 10  0  0  0  0  0  0  0  0999 V2000
    2.7760   -0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2760   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3943    1.2135    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0323    0.7500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2458    1.6317    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0323   -0.7500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2458   -1.6317    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3943   -1.2135    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8578    2.6401    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8578   -2.6401    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  2  0
  6  8  1  0
  8  2  1  0
  3  9  1  0
  8 10  1  0
M  END
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3D MOL for NP0002892 (Parabanic acid)

NP0002892
     RDKit          3D

 10 10  0  0  0  0  0  0  0  0999 V2000
   -2.5339   -1.1353    0.3556 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3835   -0.6361    0.1567 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1447   -1.3006    0.0670 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8310   -0.5126   -0.1395 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1856   -0.8822   -0.2745 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2860    0.8384   -0.2096 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9285    1.9047   -0.4022 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1220    0.7513   -0.0204 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.7870   -0.5683    0.4781 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8341    1.5407   -0.0110 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  2  0
  6  8  1  0
  8  2  1  0
  5  9  1  0
  8 10  1  0
M  END
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3D SDF for NP0002892 (Parabanic acid)


     RDKit          2D

 10 10  0  0  0  0  0  0  0  0999 V2000
    2.7760   -0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2760   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3943    1.2135    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0323    0.7500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2458    1.6317    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0323   -0.7500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2458   -1.6317    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3943   -1.2135    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8578    2.6401    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8578   -2.6401    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  2  0
  6  8  1  0
  8  2  1  0
  3  9  1  0
  8 10  1  0
M  END
> <DATABASE_ID>
NP0002892

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC1=NC(=O)NC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C3H2N2O3/c6-1-2(7)5-3(8)4-1/h(H2,4,5,6,7,8)

> <INCHI_KEY>
ZFLIKDUSUDBGCD-UHFFFAOYSA-N

> <FORMULA>
C3H2N2O3

> <MOLECULAR_WEIGHT>
114.06

> <EXACT_MASS>
114.006541932

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
10

> <JCHEM_AVERAGE_POLARIZABILITY>
8.460719559594729

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
4-hydroxy-2,5-dihydro-1H-imidazole-2,5-dione

> <ALOGPS_LOGP>
-1.50

> <JCHEM_LOGP>
-0.8361765866666665

> <ALOGPS_LOGS>
-0.56

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.312396454660675

> <JCHEM_PKA_STRONGEST_ACIDIC>
5.085598550933044

> <JCHEM_PKA_STRONGEST_BASIC>
-6.0108758429456435

> <JCHEM_POLAR_SURFACE_AREA>
78.76

> <JCHEM_REFRACTIVITY>
21.7473

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.17e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-hydroxy-3H-imidazole-2,4-dione

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0002892 (Parabanic acid)

NP0002892
     RDKit          3D

 10 10  0  0  0  0  0  0  0  0999 V2000
   -2.5339   -1.1353    0.3556 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3835   -0.6361    0.1567 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1447   -1.3006    0.0670 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8310   -0.5126   -0.1395 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1856   -0.8822   -0.2745 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2860    0.8384   -0.2096 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9285    1.9047   -0.4022 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1220    0.7513   -0.0204 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.7870   -0.5683    0.4781 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8341    1.5407   -0.0110 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  2  0
  6  8  1  0
  8  2  1  0
  5  9  1  0
  8 10  1  0
M  END
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PDB for NP0002892 (Parabanic acid)

HEADER    PROTEIN                                 23-MAR-17   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-MAR-17         0                                  
HETATM    1  O   UNK     0       1.060   3.620   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       1.060   2.080   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0       2.306   1.175   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0       1.830  -0.290   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       2.735  -1.536   0.000  0.00  0.00           O+0
HETATM    6  N   UNK     0       0.290  -0.290   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0      -0.186   1.175   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -1.651   1.651   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    7                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7                                                       
CONECT    7    6    2    8                                                  
CONECT    8    7                                                            
MASTER        0    0    0    0    0    0    0    0    8    0   16    0
END
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3D PDB for NP0002892 (Parabanic acid)

COMPND    NP0002892
HETATM    1  O1  UNL     1      -2.534  -1.135   0.356  1.00  0.00           O  
HETATM    2  C1  UNL     1      -1.383  -0.636   0.157  1.00  0.00           C  
HETATM    3  N1  UNL     1      -0.145  -1.301   0.067  1.00  0.00           N  
HETATM    4  C2  UNL     1       0.831  -0.513  -0.139  1.00  0.00           C  
HETATM    5  O2  UNL     1       2.186  -0.882  -0.275  1.00  0.00           O  
HETATM    6  C3  UNL     1       0.286   0.838  -0.210  1.00  0.00           C  
HETATM    7  O3  UNL     1       0.929   1.905  -0.402  1.00  0.00           O  
HETATM    8  N2  UNL     1      -1.122   0.751  -0.020  1.00  0.00           N  
HETATM    9  H1  UNL     1       2.787  -0.568   0.478  1.00  0.00           H  
HETATM   10  H2  UNL     1      -1.834   1.541  -0.011  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    8
CONECT    3    4    4
CONECT    4    5    6
CONECT    5    9
CONECT    6    7    7    8
CONECT    8   10
END
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SMILES for NP0002892 (Parabanic acid)

OC1=NC(=O)NC1=O
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INCHI for NP0002892 (Parabanic acid)

InChI=1S/C3H2N2O3/c6-1-2(7)5-3(8)4-1/h(H2,4,5,6,7,8)
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View in JSmol
Synonyms
ValueSource
2,4,5-ImidazolidinetrioneChEBI
Imidazolidine-2,4,5-trioneChEBI
OxalylureaChEBI
ParabanateChEBI
Chemical FormulaC3H2N2O3
Average Mass114.0600 Da
Monoisotopic Mass114.00654 Da
IUPAC Name4-hydroxy-2,5-dihydro-1H-imidazole-2,5-dione
Traditional Name5-hydroxy-3H-imidazole-2,4-dione
CAS Registry NumberNot Available
SMILES
OC1=NC(=O)NC1=O
InChI Identifier
InChI=1S/C3H2N2O3/c6-1-2(7)5-3(8)4-1/h(H2,4,5,6,7,8)
InChI KeyZFLIKDUSUDBGCD-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 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 imidazolinones. These are organic compounds containing an imidazolinone moiety, which is an imidazoline ring bearing a ketone.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassAzolines
Sub ClassImidazolines
Direct ParentImidazolinones
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-1.5ALOGPS
logP-0.84ChemAxon
logS-0.56ALOGPS
pKa (Strongest Acidic)5.09ChemAxon
pKa (Strongest Basic)-6ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area78.76 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity21.75 m³·mol⁻¹ChemAxon
Polarizability8.46 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0062802
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID60473
KEGG Compound IDNot Available
BioCyc IDCPD-3685
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound67126
PDB IDNot Available
ChEBI ID74661
Good Scents IDNot Available
References
General References
  1. Ulrich EL, Akutsu H, Doreleijers JF, Harano Y, Ioannidis YE, Lin J, Livny M, Mading S, Maziuk D, Miller Z, Nakatani E, Schulte CF, Tolmie DE, Kent Wenger R, Yao H, Markley JL: BioMagResBank. Nucleic Acids Res. 2008 Jan;36(Database issue):D402-8. doi: 10.1093/nar/gkm957. Epub 2007 Nov 4. [PubMed:17984079 ]
  2. CONRAD WE: The isolation of oxamide and parabanic acid from the products of ultraviolet irradiated uracil. Radiat Res. 1954 Dec;1(6):523-9. [PubMed:13215781 ]
  3. Kaur H, Halliwell B: Action of biologically-relevant oxidizing species upon uric acid. Identification of uric acid oxidation products. Chem Biol Interact. 1990;73(2-3):235-47. doi: 10.1016/0009-2797(90)90006-9. [PubMed:2155712 ]
  4. Jena NR, Mishra PC: Formation of ring-opened and rearranged products of guanine: mechanisms and biological significance. Free Radic Biol Med. 2012 Jul 1;53(1):81-94. doi: 10.1016/j.freeradbiomed.2012.04.008. Epub 2012 Apr 21. [PubMed:22583701 ]
  5. Peuzin MC, Cadet J, Polverelli M, Teoule R: Parabanic acid and 5-hydroxy hydantoin upon gamma-irradiation of aerated aqueous solutions of uracil. Biochim Biophys Acta. 1970;209(2):573-4. doi: 10.1016/0005-2787(70)90755-0. [PubMed:5453531 ]