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Showing NP-Card for (1r,5s,6r)-5-hydroxy-3-(hydroxymethyl)-7-oxabicyclo[4.1.0]hept-3-en-2-one (NP0246039)

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Record Information
Version2.0
Created at2022-09-07 07:20:59 UTC
Updated at2022-09-07 07:20:59 UTC
NP-MRD IDNP0246039
Secondary Accession NumbersNone
Natural Product Identification
Common Name(1r,5s,6r)-5-hydroxy-3-(hydroxymethyl)-7-oxabicyclo[4.1.0]hept-3-en-2-one
Description(+)-Isoepoxydon 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 (+)-isoepoxydon 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. (1r,5s,6r)-5-hydroxy-3-(hydroxymethyl)-7-oxabicyclo[4.1.0]hept-3-en-2-one is found in Arthrinium arundinis, Pestalotiopsis longiseta, Poronia punctata and Ulva intestinalis. (1r,5s,6r)-5-hydroxy-3-(hydroxymethyl)-7-oxabicyclo[4.1.0]hept-3-en-2-one was first documented in 1979 (PMID: 43192). Based on a literature review a significant number of articles have been published on (+)-isoepoxydon (PMID: 35528279) (PMID: 30903915) (PMID: 29030968) (PMID: 26788884) (PMID: 26513254) (PMID: 24334092).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0246039 ((1r,5s,6r)-5-hydroxy-3-(hydroxymethyl)-7-oxabicyclo[4.1.0]hept-3-en-2-one)


  Mrv1652309072209212D          

 11 12  0  0  1  0            999 V2000
    2.6197    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6197    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3342    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0487    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7631    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3342    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6197   -0.4125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.6197   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9053    0.0000    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.1908    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9053    0.8250    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  3  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  6  0  0  0
  7  9  1  0  0  0  0
  9 10  1  1  0  0  0
 11 10  1  1  0  0  0
  2 11  1  0  0  0  0
  9 11  1  0  0  0  0
M  END
Download

3D MOL for NP0246039 ((1r,5s,6r)-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
    0.9854   -2.1414   -1.2168 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2676   -1.3217   -0.6217 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8387   -0.0872   -0.0644 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2578   -0.0548    0.3763 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1088   -0.3467   -0.7045 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0461    0.9599    0.0243 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3707    0.9332   -0.4144 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.0698    1.8230    0.4047 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0145   -0.4130   -0.3190 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.0082   -1.2152   -1.5076 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1734   -1.5809   -0.4677 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.4452   -0.8503    1.1555 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4871    0.9300    0.8276 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6659    0.4385   -0.9150 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4762    1.8860    0.4468 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4528    1.3111   -1.4737 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0672    2.7519    0.0370 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9618   -0.5184    0.2508 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4603   -2.5039    0.0798 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  6
  8 17  1  0
  9 18  1  1
 11 19  1  1
M  END
Download

3D SDF for NP0246039 ((1r,5s,6r)-5-hydroxy-3-(hydroxymethyl)-7-oxabicyclo[4.1.0]hept-3-en-2-one)


  Mrv1652309072209212D          

 11 12  0  0  1  0            999 V2000
    2.6197    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6197    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3342    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0487    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7631    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3342    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6197   -0.4125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.6197   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9053    0.0000    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.1908    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9053    0.8250    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  3  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  6  0  0  0
  7  9  1  0  0  0  0
  9 10  1  1  0  0  0
 11 10  1  1  0  0  0
  2 11  1  0  0  0  0
  9 11  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0246039

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OCC1=C[C@H](O)[C@H]2O[C@H]2C1=O

> <INCHI_IDENTIFIER>
InChI=1S/C7H8O4/c8-2-3-1-4(9)6-7(11-6)5(3)10/h1,4,6-9H,2H2/t4-,6+,7-/m0/s1

> <INCHI_KEY>
VTLJDPHPVHSVGR-JHYUDYDFSA-N

> <FORMULA>
C7H8O4

> <MOLECULAR_WEIGHT>
156.137

> <EXACT_MASS>
156.042258738

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
19

> <JCHEM_AVERAGE_POLARIZABILITY>
14.16419431867837

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1R,5S,6R)-5-hydroxy-3-(hydroxymethyl)-7-oxabicyclo[4.1.0]hept-3-en-2-one

> <JCHEM_LOGP>
-1.1024650153333333

> <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>
36.023599999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1R,5S,6R)-5-hydroxy-3-(hydroxymethyl)-7-oxabicyclo[4.1.0]hept-3-en-2-one

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0246039 ((1r,5s,6r)-5-hydroxy-3-(hydroxymethyl)-7-oxabicyclo[4.1.0]hept-3-en-2-one)

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PDB for NP0246039 ((1r,5s,6r)-5-hydroxy-3-(hydroxymethyl)-7-oxabicyclo[4.1.0]hept-3-en-2-one)
HEADER    PROTEIN                                 07-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   07-SEP-22         0                                  
HETATM    1  O   UNK     0       4.890   3.850   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       4.890   2.310   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       6.224   1.540   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       7.558   2.310   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       8.891   1.540   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       6.224   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.890  -0.770   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       4.890  -2.310   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       3.556   0.000   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       2.223   0.770   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       3.556   1.540   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   11                                                  
CONECT    3    2    4    6                                                  
CONECT    4    3    5                                                       
CONECT    5    4                                                            
CONECT    6    3    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10   11                                                  
CONECT   10    9   11                                                       
CONECT   11   10    2    9                                                  
MASTER        0    0    0    0    0    0    0    0   11    0   24    0
END

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3D PDB for NP0246039 ((1r,5s,6r)-5-hydroxy-3-(hydroxymethyl)-7-oxabicyclo[4.1.0]hept-3-en-2-one)
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SMILES for NP0246039 ((1r,5s,6r)-5-hydroxy-3-(hydroxymethyl)-7-oxabicyclo[4.1.0]hept-3-en-2-one)
OCC1=C[C@H](O)[C@H]2O[C@H]2C1=O
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INCHI for NP0246039 ((1r,5s,6r)-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/t4-,6+,7-/m0/s1
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View in JSmol
Synonyms
ValueSource
(1R,5S,6R)-5-Hydroxy-3-(hydroxymethyl)-7-oxabicyclo[4.1.0]hept-3-en-2-oneChEBI
IsoepoxydonChEBI
5,6-Epoxy-4-hydroxy-2-hydroxymethylcyclohex-2- en-1-oneMeSH
Chemical FormulaC7H8O4
Average Mass156.1370 Da
Monoisotopic Mass156.04226 Da
IUPAC Name(1R,5S,6R)-5-hydroxy-3-(hydroxymethyl)-7-oxabicyclo[4.1.0]hept-3-en-2-one
Traditional Name(1R,5S,6R)-5-hydroxy-3-(hydroxymethyl)-7-oxabicyclo[4.1.0]hept-3-en-2-one
CAS Registry NumberNot Available
SMILES
OCC1=C[C@H](O)[C@H]2O[C@H]2C1=O
InChI Identifier
InChI=1S/C7H8O4/c8-2-3-1-4(9)6-7(11-6)5(3)10/h1,4,6-9H,2H2/t4-,6+,7-/m0/s1
InChI KeyVTLJDPHPVHSVGR-JHYUDYDFSA-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
Pestalotiopsis longisetaLOTUS Database
Poronia punctataLOTUS 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-1.1ChemAxon
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
Polarizability14.16 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 IDC00044399  
Chemspider ID293929  
KEGG Compound IDNot Available
BioCyc IDCPD-16723  
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound331736  
PDB IDNot Available
ChEBI ID145109  
Good Scents IDNot Available
References
General References
  1. Fu R, Tang W, Zhang H, Zhang Y, Wang D, Chen W: Study on the mechanism of inhibiting patulin production by fengycin. Open Life Sci. 2022 Apr 19;17(1):372-379. doi: 10.1515/biol-2022-0041.  eCollection 2022. [PubMed:35528279  ] 
  2. Frisch LM, Niessen L: Development and optimization of a group-specific loop-mediated isothermal amplification (LAMP) assay for the detection of patulin-producing Penicillium species. Int J Food Microbiol. 2019 Jun 2;298:20-30. doi:  10.1016/j.ijfoodmicro.2019.03.010. Epub 2019 Mar 15. [PubMed:30903915  ] 
  3. Wang Y, Feng K, Liu B, Zhang Z, Wei J, Yuan Y, Yue T: Mycoflora assessment, growth and toxigenic features of patulin-producers in kiwifruit in China. J Sci Food Agric. 2018 May;98(7):2573-2581. doi: 10.1002/jsfa.8747. Epub 2017 Nov  28. [PubMed:29030968  ] 
  4. De Clercq N, Vlaemynck G, Van Pamel E, Van Weyenberg S, Herman L, Devlieghere F, De Meulenaer B, Van Coillie E: Isoepoxydon dehydrogenase (idh) gene expression in relation to patulin production by Penicillium expansum under different temperature and atmosphere. Int J Food Microbiol. 2016 Mar 2;220:50-7. doi:  10.1016/j.ijfoodmicro.2016.01.004. Epub 2016 Jan 9. [PubMed:26788884  ] 
  5. Rharmitt S, Hafidi M, Hajjaj H, Scordino F, Giosa D, Giuffre L, Barreca D, Criseo G, Romeo O: Molecular characterization of patulin producing and non-producing Penicillium species in apples from Morocco. Int J Food Microbiol. 2016 Jan 18;217:137-40. doi:  10.1016/j.ijfoodmicro.2015.10.019. Epub 2015 Oct 19. [PubMed:26513254  ] 
  6. Snini SP, Tadrist S, Laffitte J, Jamin EL, Oswald IP, Puel O: The gene PatG involved in the biosynthesis pathway of patulin, a food-borne mycotoxin, encodes a 6-methylsalicylic acid decarboxylase. Int J Food Microbiol. 2014 Feb 3;171:77-83. doi:  10.1016/j.ijfoodmicro.2013.11.020. Epub 2013 Nov 27. [PubMed:24334092  ] 
  7. Rodriguez A, Luque MI, Andrade MJ, Rodriguez M, Asensio MA, Cordoba JJ: Development of real-time PCR methods to quantify patulin-producing molds in food products. Food Microbiol. 2011 Sep;28(6):1190-9. doi: 10.1016/j.fm.2011.04.004. Epub 2011  Apr 23. [PubMed:21645819  ] 
  8. Artigot MP, Loiseau N, Laffitte J, Mas-Reguieg L, Tadrist S, Oswald IP, Puel O: Molecular cloning and functional characterization of two CYP619 cytochrome P450s involved in biosynthesis of patulin in Aspergillus clavatus. Microbiology (Reading). 2009 May;155(Pt 5):1738-1747. doi:  10.1099/mic.0.024836-0. Epub 2009 Apr 21. [PubMed:19383676  ] 
  9. Paterson RR: The isoepoxydon dehydrogenase gene PCR profile is useful in fungal taxonomy. Rev Iberoam Micol. 2007 Dec 31;24(4):289-93. [PubMed:18095762  ] 
  10. Dombrink-Kurtzman MA, McGovern AE: Species-specific identification of penicillium linked to patulin contamination. J Food Prot. 2007 Nov;70(11):2646-50. doi: 10.4315/0362-028x-70.11.2646. [PubMed:18044450  ] 
  11. Dombrink-Kurtzman MA: A gene having sequence homology to isoamyl alcohol oxidase is transcribed during patulin production in Penicillium griseofulvum. Curr Microbiol. 2008 Mar;56(3):224-8. doi: 10.1007/s00284-007-9061-0. Epub 2007  Nov 14. [PubMed:18000703  ] 
  12. Paterson RR, Venancio A, Lima N: A practical approach for identifications based on mycotoxin characters of Penicillium. Rev Iberoam Micol. 2006 Sep;23(3):155-9. doi: 10.1016/s1130-1406(06)70036-5. [PubMed:17196022  ] 
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  22. LOTUS database [Link]