NP-MRD: Showing NP-Card for 3-hydroxy-5α,6α-epoxy-β-ionone (NP0331996)

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Record Information

Version

2.0

Created at

2023-10-17 16:22:57 UTC

Updated at

2024-09-03 04:17:39 UTC

NP-MRD ID

NP0331996

Natural Product DOI

https://doi.org/10.57994/1117

Secondary Accession Numbers

None

Natural Product Identification

Common Name

3-hydroxy-5α,6α-epoxy-β-ionone

Description

CHEMBL2392397 belongs to the class of organic compounds known as oxepanes. Oxepanes are compounds containing an oxepane ring, which is a seven-member saturated aliphatic heterocycle with one oxygen and six carbon atoms. 3-hydroxy-5α,6α-epoxy-β-ionone was first documented in 2023 (PMID: 37714249). Based on a literature review very few articles have been published on CHEMBL2392397.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 36 37  0  0  0  0  0  0  0  0999 V2000
    4.8075    0.3967   -0.3404 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7010   -0.4939    0.0797 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9112   -1.6173    0.6235 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3345   -0.0672   -0.1378 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2886   -0.8139    0.2135 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1206   -0.4518    0.0267 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7962   -1.1445   -1.1077 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0956   -1.5124    0.2052 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7250   -2.9385    0.4867 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4187   -1.1408    0.8220 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9349    0.0573    0.0801 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.1971    0.3885    0.5804 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9997    1.1699    0.4598 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5846    0.9429    0.0093 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2714    1.8816    0.8612 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5912    1.4558   -1.4429 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7004    0.3072    0.3120 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4358    1.4545   -0.2287 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0132    0.2027   -1.4010 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1303    0.8672   -0.5901 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5543   -1.7663    0.6758 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7941   -3.2085    1.5628 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4831   -3.5979   -0.0231 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2515   -3.2446    0.1350 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1164   -1.9811    0.8052 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1848   -0.8283    1.8825 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9638   -0.1204   -0.9927 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3695    1.3252    0.3157 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4183    2.1076    0.0285 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0245    1.2964    1.5619 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3246    2.4704    1.5907 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0042    1.3207    1.4772 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7641    2.6629    0.2208 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5204    0.9988   -1.8957 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2352    1.0823   -2.0312 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7398    2.5389   -1.4480 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  2  4  1  0
  4  5  2  0
  6  5  1  6
  6  7  1  0
  7  8  1  0
  8  9  1  6
  8 10  1  0
 10 11  1  0
 11 12  1  0
 11 13  1  0
 13 14  1  0
 14 15  1  0
 14 16  1  0
  8  6  1  0
 14  6  1  0
  1 17  1  0
  1 18  1  0
  1 19  1  0
  4 20  1  0
  5 21  1  0
  9 22  1  0
  9 23  1  0
  9 24  1  0
 10 25  1  0
 10 26  1  0
 11 27  1  6
 12 28  1  0
 13 29  1  0
 13 30  1  0
 15 31  1  0
 15 32  1  0
 15 33  1  0
 16 34  1  0
 16 35  1  0
 16 36  1  0
M  END


  Mrv1652309042217342D          

 16 17  0  0  1  0            999 V2000
   -1.9987   -2.2539    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1737   -2.2539    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7612   -2.9684    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7612   -1.5395    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0638   -1.5395    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4763   -0.8250    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.2382   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4763   -0.0000    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0638    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1908    0.4125    0.0000 C   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
    2.6197    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  0  0  0  0  0  0  0  0  0  0
    1.1908   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5781   -1.9659    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8035   -1.9659    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  2  4  1  0  0  0  0
  4  5  2  0  0  0  0
  6  5  1  1  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  6  8  1  0  0  0  0
  8  9  1  1  0  0  0
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  1  0  0  0
 11 13  1  0  0  0  0
 13 14  1  0  0  0  0
  6 14  1  0  0  0  0
 14 15  1  0  0  0  0
 14 16  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0331996

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(=O)\C=C\[C@@]12O[C@]1(C)C[C@@H](O)CC2(C)C

> <INCHI_IDENTIFIER>
InChI=1S/C13H20O3/c1-9(14)5-6-13-11(2,3)7-10(15)8-12(13,4)16-13/h5-6,10,15H,7-8H2,1-4H3/b6-5+/t10-,12+,13-/m0/s1

> <INCHI_KEY>
VYKLRWGPNUVKNC-IRIVYCKASA-N

> <FORMULA>
C13H20O3

> <MOLECULAR_WEIGHT>
224.3

> <EXACT_MASS>
224.141244504

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
36

> <JCHEM_AVERAGE_POLARIZABILITY>
24.611934363410036

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(3E)-4-[(1S,4S,6R)-4-hydroxy-2,2,6-trimethyl-7-oxabicyclo[4.1.0]heptan-1-yl]but-3-en-2-one

> <JCHEM_LOGP>
1.3423136756666667

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
19.83436969917283

> <JCHEM_PKA_STRONGEST_ACIDIC>
15.139675228557245

> <JCHEM_PKA_STRONGEST_BASIC>
-2.7377022179288097

> <JCHEM_POLAR_SURFACE_AREA>
49.83

> <JCHEM_REFRACTIVITY>
62.1797

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(3E)-4-[(1S,4S,6R)-4-hydroxy-2,2,6-trimethyl-7-oxabicyclo[4.1.0]heptan-1-yl]but-3-en-2-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 04-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-22         0                                  
HETATM    1  C   UNK     0      -3.731  -4.207   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -2.191  -4.207   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      -1.421  -5.541   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      -1.421  -2.874   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.119  -2.874   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.889  -1.540   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      -0.445  -0.770   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       0.889  -0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.119   1.334   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.223   0.770   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       3.556  -0.000   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       4.890   0.770   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       3.556  -1.540   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       2.223  -2.310   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       2.946  -3.670   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       1.500  -3.670   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7    8   14                                             
CONECT    7    6    8                                                       
CONECT    8    7    6    9   10                                             
CONECT    9    8                                                            
CONECT   10    8   11                                                       
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14                                                       
CONECT   14   13    6   15   16                                             
CONECT   15   14                                                            
CONECT   16   14                                                            
MASTER        0    0    0    0    0    0    0    0   16    0   34    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₃H₂₀O₃

Average Mass

224.3000 Da

Monoisotopic Mass

224.14124 Da

IUPAC Name

(3E)-4-[(1S,4S,6R)-4-hydroxy-2,2,6-trimethyl-7-oxabicyclo[4.1.0]heptan-1-yl]but-3-en-2-one

Traditional Name

(3E)-4-[(1S,4S,6R)-4-hydroxy-2,2,6-trimethyl-7-oxabicyclo[4.1.0]heptan-1-yl]but-3-en-2-one

CAS Registry Number

Not Available

SMILES

CC(=O)\C=C\[C@@]12O[C@]1(C)C[C@@H](O)CC2(C)C

InChI Identifier

InChI=1S/C13H20O3/c1-9(14)5-6-13-11(2,3)7-10(15)8-12(13,4)16-13/h5-6,10,15H,7-8H2,1-4H3/b6-5+/t10-,12+,13-/m0/s1

InChI Key

VYKLRWGPNUVKNC-IRIVYCKASA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, CD3OD, experimental)	wuhonghua2011@tjutcm.edu.cn	Tianjin University of Traditional Chinese Medicine	Hong-Hua Wu	2023-10-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, CD3OD, experimental)	wuhonghua2011@tjutcm.edu.cn	Tianjin University of Traditional Chinese Medicine	Hong-Hua Wu	2023-10-17	View Spectrum

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹H NMR Spectrum (1D, 600, CD₃OD, simulated)	wuhonghua2011@tjutcm.edu.cn	Tianjin University of Traditional Chinese Medicine	Hong-Hua Wu	2024-05-14	View Spectrum

Species

Species of Origin

Species Name	Source	Reference
erecta		Not Available

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as oxepanes. Oxepanes are compounds containing an oxepane ring, which is a seven-member saturated aliphatic heterocycle with one oxygen and six carbon atoms.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Oxepanes

Sub Class

Not Available

Direct Parent

Oxepanes

Alternative Parents

Substituents

Oxepane
Acryloyl-group
Cyclic alcohol
Enone
Alpha,beta-unsaturated ketone
Secondary alcohol
Ketone
Ether
Oxirane
Dialkyl ether
Oxacycle
Organic oxygen compound
Organooxygen compound
Alcohol
Carbonyl group
Hydrocarbon derivative
Organic oxide
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

Not Available

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
logP	1.34	ChemAxon
pKa (Strongest Acidic)	15.14	ChemAxon
pKa (Strongest Basic)	-2.7	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	49.83 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	62.18 m³·mol⁻¹	ChemAxon
Polarizability	24.61 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

10364085

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

14605580

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for 3-hydroxy-5α,6α-epoxy-β-ionone (NP0331996)

MOL for NP0331996 (3-hydroxy-5α,6α-epoxy-β-ionone)

3D MOL for NP0331996 (3-hydroxy-5α,6α-epoxy-β-ionone)

3D SDF for NP0331996 (3-hydroxy-5α,6α-epoxy-β-ionone)

3D-SDF for NP0331996 (3-hydroxy-5α,6α-epoxy-β-ionone)

PDB for NP0331996 (3-hydroxy-5α,6α-epoxy-β-ionone)

3D PDB for NP0331996 (3-hydroxy-5α,6α-epoxy-β-ionone)

SMILES for NP0331996 (3-hydroxy-5α,6α-epoxy-β-ionone)

INCHI for NP0331996 (3-hydroxy-5α,6α-epoxy-β-ionone)

Structure for NP0331996 (3-hydroxy-5α,6α-epoxy-β-ionone)

3D Structure for NP0331996 (3-hydroxy-5α,6α-epoxy-β-ionone)