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Showing NP-Card for 2,3-Dihydroxy-2,4-cyclopentadien-1-one (NP0086449)

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Record Information
Version2.0
Created at2022-04-29 06:45:00 UTC
Updated at2022-04-29 06:45:00 UTC
NP-MRD IDNP0086449
Secondary Accession NumbersNone
Natural Product Identification
Common Name2,3-Dihydroxy-2,4-cyclopentadien-1-one
Description2,3-Dihydroxy-2,4-cyclopentadien-1-one belongs to the class of organic compounds known as vinylogous acids. These are organic compounds containing a hydroxyl group, which is indirectly attached to a carbonyl via an intervening vinyl (>C=C<) moiety. 2,3-Dihydroxy-2,4-cyclopentadien-1-one is an extremely weak basic (essentially neutral) compound (based on its pKa). Outside of the human body, 2,3-Dihydroxy-2,4-cyclopentadien-1-one has been detected, but not quantified in, a few different foods, such as herbs and spices, pulses, and tea. 2,3-Dihydroxy-2,4-cyclopentadien-1-one is found in Trifolium repens . This could make 2,3-dihydroxy-2,4-cyclopentadien-1-one a potential biomarker for the consumption of these foods.
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0086449 (2,3-Dihydroxy-2,4-cyclopentadien-1-one)


  Mrv0541 05061311092D          

  8  8  0  0  0  0            999 V2000
    0.7062   -0.6632    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9611    0.1214    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1188   -0.6632    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2937    0.6064    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3738    0.1214    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6037   -1.3306    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2937    1.4314    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1584    0.3764    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  2  0  0  0  0
  5  4  1  0  0  0  0
  6  3  1  0  0  0  0
  7  4  2  0  0  0  0
  8  5  1  0  0  0  0
M  END
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3D MOL for NP0086449 (2,3-Dihydroxy-2,4-cyclopentadien-1-one)

     RDKit          3D

 12 12  0  0  0  0  0  0  0  0999 V2000
   -1.7448   -1.9828    0.0918 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1098   -0.9073   -0.0210 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6437    0.4369   -0.2122 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5981    1.2499   -0.2761 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6248    0.4935   -0.1335 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9488    0.9439   -0.1407 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3354   -0.8092    0.0213 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2436   -1.8447    0.1874 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6807    0.7341   -0.2893 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6557    2.3204   -0.4145 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3342    1.4487   -0.9113 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9460   -2.0834   -0.4897 H   0  0  0  0  0  0  0  0  0  0  0  0
  6  5  1  0
  5  7  2  0
  7  8  1  0
  7  2  1  0
  2  1  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  6 11  1  0
  8 12  1  0
  3  9  1  0
  4 10  1  0
M  END
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3D SDF for NP0086449 (2,3-Dihydroxy-2,4-cyclopentadien-1-one)


  Mrv0541 05061311092D          

  8  8  0  0  0  0            999 V2000
    0.7062   -0.6632    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9611    0.1214    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1188   -0.6632    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2937    0.6064    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3738    0.1214    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6037   -1.3306    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2937    1.4314    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1584    0.3764    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  2  0  0  0  0
  5  4  1  0  0  0  0
  6  3  1  0  0  0  0
  7  4  2  0  0  0  0
  8  5  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0086449

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC1=C(O)C(=O)C=C1

> <INCHI_IDENTIFIER>
InChI=1S/C5H4O3/c6-3-1-2-4(7)5(3)8/h1-2H,(H2,6,7,8)

> <INCHI_KEY>
RUOZZXHSVNXNKB-UHFFFAOYSA-N

> <FORMULA>
C5H4O3

> <MOLECULAR_WEIGHT>
112.0835

> <EXACT_MASS>
112.016043994

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
9.718920914289223

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2,3-dihydroxycyclopenta-2,4-dien-1-one

> <ALOGPS_LOGP>
-0.93

> <JCHEM_LOGP>
-0.15023200133333328

> <ALOGPS_LOGS>
0.20

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.444245165090596

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.786918059033601

> <JCHEM_PKA_STRONGEST_BASIC>
-3.815521741386715

> <JCHEM_POLAR_SURFACE_AREA>
57.53

> <JCHEM_REFRACTIVITY>
29.692699999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.77e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2,3-dihydroxycyclopenta-2,4-dien-1-one

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0086449 (2,3-Dihydroxy-2,4-cyclopentadien-1-one)

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PDB for NP0086449 (2,3-Dihydroxy-2,4-cyclopentadien-1-one)
HEADER    PROTEIN                                 06-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAY-13         0                                  
HETATM    1  C   UNK     0       1.318  -1.238   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.794   0.227   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.222  -1.238   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.548   1.132   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.698   0.227   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -1.127  -2.484   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       0.548   2.672   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      -2.162   0.703   0.000  0.00  0.00           O+0
CONECT    1    2    3                                                       
CONECT    2    1    4                                                       
CONECT    3    1    5    6                                                  
CONECT    4    2    5    7                                                  
CONECT    5    3    4    8                                                  
CONECT    6    3                                                            
CONECT    7    4                                                            
CONECT    8    5                                                            
MASTER        0    0    0    0    0    0    0    0    8    0   16    0
END

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3D PDB for NP0086449 (2,3-Dihydroxy-2,4-cyclopentadien-1-one)
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SMILES for NP0086449 (2,3-Dihydroxy-2,4-cyclopentadien-1-one)
OC1=C(O)C(=O)C=C1
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INCHI for NP0086449 (2,3-Dihydroxy-2,4-cyclopentadien-1-one)
InChI=1S/C5H4O3/c6-3-1-2-4(7)5(3)8/h1-2H,(H2,6,7,8)
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View in JSmol
SynonymsNot Available
Chemical FormulaC5H4O3
Average Mass112.0835 Da
Monoisotopic Mass112.01604 Da
IUPAC Name2,3-dihydroxycyclopenta-2,4-dien-1-one
Traditional Name2,3-dihydroxycyclopenta-2,4-dien-1-one
CAS Registry NumberNot Available
SMILES
OC1=C(O)C(=O)C=C1
InChI Identifier
InChI=1S/C5H4O3/c6-3-1-2-4(7)5(3)8/h1-2H,(H2,6,7,8)
InChI KeyRUOZZXHSVNXNKB-UHFFFAOYSA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Trifolium repensPlant
Chemical Taxonomy
Description Belongs to the class of organic compounds known as vinylogous acids. These are organic compounds containing a hydroxyl group, which is indirectly attached to a carbonyl via an intervening vinyl (>C=C<) moiety.
KingdomOrganic compounds  
Super ClassOrganic acids and derivatives  
ClassVinylogous acids  
Sub ClassNot Available
Direct ParentVinylogous acids  
Alternative Parents
Substituents
  • Vinylogous acid
    • 

  • Cyclic ketone
    • 

  • Ketone
    • 

  • Enediol
    • 

  • Organic oxygen compound
    • 

  • Organic oxide
    • 

  • Hydrocarbon derivative
    • 

  • Organooxygen compound
    • 

  • Carbonyl group
    • 

  • Aliphatic homomonocyclic compound
Molecular FrameworkAliphatic homomonocyclic 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-0.93ALOGPS
logP-0.15ChemAxon
logS0.2ALOGPS
pKa (Strongest Acidic)7.79ChemAxon
pKa (Strongest Basic)-3.8ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area57.53 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity29.69 m³·mol⁻¹ChemAxon
Polarizability9.72 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0039437  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB019033  
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound14412554  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General ReferencesNot Available