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Showing NP-Card for 5-hydroxy-3-(hydroxymethyl)-7-oxabicyclo[4.1.0]hept-3-en-2-one (NP0297204)

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Record Information
Version2.0
Created at2022-09-10 07:19:29 UTC
Updated at2022-09-10 07:19:29 UTC
NP-MRD IDNP0297204
Secondary Accession NumbersNone
Natural Product Identification
Common Name5-hydroxy-3-(hydroxymethyl)-7-oxabicyclo[4.1.0]hept-3-en-2-one
Description5-Hydroxy-3-(hydroxymethyl)-7-oxabicyclo[4.1.0]Hept-3-en-2-one belongs to the class of organic compounds known as cyclohexenones. Cyclohexenones are compounds containing a cylohexenone moiety, which is a six-membered aliphatic ring that carries a ketone and has one endocyclic double bond. 5-hydroxy-3-(hydroxymethyl)-7-oxabicyclo[4.1.0]hept-3-en-2-one is found in Arthrinium arundinis, Didymella glomerata, Pestalotiopsis longiseta, Stagonosporopsis ligulicola and Ulva intestinalis. 5-Hydroxy-3-(hydroxymethyl)-7-oxabicyclo[4.1.0]Hept-3-en-2-one is an extremely weak basic (essentially neutral) compound (based on its pKa).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0297204 (5-hydroxy-3-(hydroxymethyl)-7-oxabicyclo[4.1.0]hept-3-en-2-one)


  Mrv1533004181501512D          

 11 12  0  0  0  0            999 V2000
    3.5724    2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    0.4125    0.0000 C   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
    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 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  7  9  1  0  0  0  0
  9 10  1  0  0  0  0
  3 10  1  0  0  0  0
 10 11  2  0  0  0  0
M  END
Download

3D MOL for NP0297204 (5-hydroxy-3-(hydroxymethyl)-7-oxabicyclo[4.1.0]hept-3-en-2-one)

     RDKit          3D

 19 20  0  0  0  0  0  0  0  0999 V2000
    1.1690   -2.1688   -0.7313 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3603   -1.2152   -0.5830 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8319    0.0988   -0.1299 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2579    0.4845   -0.3392 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1175   -0.3955    0.3051 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0419    0.9083    0.4588 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4473    0.5895    0.6921 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.2288    1.7194    0.3540 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9764   -0.5581   -0.0891 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.7537   -0.3329   -1.5327 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0892   -1.3474   -0.8484 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.4561    0.5376   -1.4346 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4175    1.4901    0.0962 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2659   -1.2354   -0.1988 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3410    1.8676    0.7792 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6206    0.4000    1.7782 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6711    2.3921   -0.0857 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9973   -0.8685    0.1552 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3904   -2.3661   -1.1626 H   0  0  0  0  0  0  0  0  0  0  0  0
  5  4  1  0
  4  3  1  0
  3  6  2  0
  6  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
 10 11  1  0
 11  2  1  0
  2  1  2  0
  2  3  1  0
 11  9  1  0
  5 14  1  0
  4 12  1  0
  4 13  1  0
  6 15  1  0
  7 16  1  1
  8 17  1  0
  9 18  1  6
 11 19  1  6
M  END
Download

3D SDF for NP0297204 (5-hydroxy-3-(hydroxymethyl)-7-oxabicyclo[4.1.0]hept-3-en-2-one)


  Mrv1533004181501512D          

 11 12  0  0  0  0            999 V2000
    3.5724    2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    0.4125    0.0000 C   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
    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 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  7  9  1  0  0  0  0
  9 10  1  0  0  0  0
  3 10  1  0  0  0  0
 10 11  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0297204

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OCC1=CC(O)C2OC2C1=O

> <INCHI_IDENTIFIER>
InChI=1S/C7H8O4/c8-2-3-1-4(9)6-7(11-6)5(3)10/h1,4,6-9H,2H2

> <INCHI_KEY>
VTLJDPHPVHSVGR-UHFFFAOYSA-N

> <FORMULA>
C7H8O4

> <MOLECULAR_WEIGHT>
156.137

> <EXACT_MASS>
156.042258738

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
19

> <JCHEM_AVERAGE_POLARIZABILITY>
14.170419266593706

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
5-hydroxy-3-(hydroxymethyl)-7-oxabicyclo[4.1.0]hept-3-en-2-one

> <ALOGPS_LOGP>
-1.54

> <JCHEM_LOGP>
-1.1024650153333333

> <ALOGPS_LOGS>
0.45

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.97752759158228

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.63076313085298

> <JCHEM_PKA_STRONGEST_BASIC>
-2.8219917495965676

> <JCHEM_POLAR_SURFACE_AREA>
70.06

> <JCHEM_REFRACTIVITY>
36.0236

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.36e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-hydroxy-3-(hydroxymethyl)-7-oxabicyclo[4.1.0]hept-3-en-2-one

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0297204 (5-hydroxy-3-(hydroxymethyl)-7-oxabicyclo[4.1.0]hept-3-en-2-one)

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PDB for NP0297204 (5-hydroxy-3-(hydroxymethyl)-7-oxabicyclo[4.1.0]hept-3-en-2-one)
HEADER    PROTEIN                                 18-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   18-APR-15         0                                  
HETATM    1  O   UNK     0       6.668   5.390   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       6.668   3.850   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.335   3.080   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.001   0.770   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       4.001  -0.770   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       1.334   2.310   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       2.667   3.080   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.001   3.850   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       4.001   5.390   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   10                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8    9                                                  
CONECT    8    7    9                                                       
CONECT    9    8    7   10                                                  
CONECT   10    9    3   11                                                  
CONECT   11   10                                                            
MASTER        0    0    0    0    0    0    0    0   11    0   24    0
END

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3D PDB for NP0297204 (5-hydroxy-3-(hydroxymethyl)-7-oxabicyclo[4.1.0]hept-3-en-2-one)
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SMILES for NP0297204 (5-hydroxy-3-(hydroxymethyl)-7-oxabicyclo[4.1.0]hept-3-en-2-one)
OCC1=CC(O)C2OC2C1=O
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INCHI for NP0297204 (5-hydroxy-3-(hydroxymethyl)-7-oxabicyclo[4.1.0]hept-3-en-2-one)
InChI=1S/C7H8O4/c8-2-3-1-4(9)6-7(11-6)5(3)10/h1,4,6-9H,2H2
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View in JSmol
SynonymsNot Available
Chemical FormulaC7H8O4
Average Mass156.1370 Da
Monoisotopic Mass156.04226 Da
IUPAC Name5-hydroxy-3-(hydroxymethyl)-7-oxabicyclo[4.1.0]hept-3-en-2-one
Traditional Name5-hydroxy-3-(hydroxymethyl)-7-oxabicyclo[4.1.0]hept-3-en-2-one
CAS Registry NumberNot Available
SMILES
OCC1=CC(O)C2OC2C1=O
InChI Identifier
InChI=1S/C7H8O4/c8-2-3-1-4(9)6-7(11-6)5(3)10/h1,4,6-9H,2H2
InChI KeyVTLJDPHPVHSVGR-UHFFFAOYSA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Arthrinium arundinisLOTUS Database
Didymella glomerataLOTUS Database
Pestalotiopsis longisetaLOTUS Database
Stagonosporopsis ligulicolaLOTUS Database
Ulva intestinalisLOTUS Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as cyclohexenones. Cyclohexenones are compounds containing a cylohexenone moiety, which is a six-membered aliphatic ring that carries a ketone and has one endocyclic double bond.
KingdomOrganic compounds  
Super ClassOrganic oxygen compounds  
ClassOrganooxygen compounds  
Sub ClassCarbonyl compounds  
Direct ParentCyclohexenones  
Alternative Parents
Substituents
  • Cyclohexenone
    • 

  • Secondary alcohol
    • 

  • Oxacycle
    • 

  • Organoheterocyclic compound
    • 

  • Ether
    • 

  • Oxirane
    • 

  • Dialkyl ether
    • 

  • Organic oxide
    • 

  • Hydrocarbon derivative
    • 

  • Primary alcohol
    • 

  • Alcohol
    • 

  • Aliphatic heteropolycyclic compound
Molecular FrameworkAliphatic heteropolycyclic 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-1.1ChemAxon
logS0.45ALOGPS
pKa (Strongest Acidic)13.63ChemAxon
pKa (Strongest Basic)-2.8ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area70.06 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity36.02 m³·mol⁻¹ChemAxon
Polarizability14.17 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound185584  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. LOTUS database [Link]