NP-MRD: Showing NP-Card for (-)-dehydrovomifoliol (NP0276016)

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Record Information

Version

2.0

Created at

2022-09-08 23:57:27 UTC

Updated at

2022-09-08 23:57:27 UTC

NP-MRD ID

NP0276016

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(-)-dehydrovomifoliol

Description

(6R)-dehydrovomifoliol belongs to the class of organic compounds known as sesquiterpenoids. These are terpenes with three consecutive isoprene units. (-)-dehydrovomifoliol is found in Helianthus heterophyllus and Viburnum dilatatum. (-)-dehydrovomifoliol was first documented in 2018 (PMID: 30111024). Based on a literature review very few articles have been published on (6R)-dehydrovomifoliol.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 34 34  0  0  0  0  0  0  0  0999 V2000
    4.5098   -0.5971    0.4028 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2432   -0.0111    0.8915 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1796    0.5630    2.0192 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0230   -0.0765    0.0861 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8819    0.4436    0.5104 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3720    0.3879   -0.2938 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0018    0.4329   -1.6360 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2373    1.5236    0.0465 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6178    2.8734    0.2653 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5463    1.4575    0.1799 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2106    0.1631   -0.0221 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3641   -0.0677    0.4215 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4134   -0.8363   -0.7851 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0811   -0.9333   -0.0729 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3536   -1.1998    1.3882 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2782   -2.0726   -0.6432 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4235   -1.7148    0.5050 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3386   -0.2326    1.0527 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6904   -0.3849   -0.6610 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0651   -0.5595   -0.8691 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8899    0.9200    1.4799 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6216    1.2217   -1.7123 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8263    3.4857   -0.6589 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4608    2.7608    0.4063 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1219    3.4008    1.1186 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1346    2.3286    0.4325 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2857   -0.4132   -1.8181 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9214   -1.8119   -0.8737 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1462   -2.0025    1.4161 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7753   -0.3361    1.9197 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4333   -1.5789    1.9160 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9048   -2.9658   -0.8423 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5554   -2.3858   -0.0130 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1392   -1.7821   -1.6476 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
  5  6  1  0
  6  7  1  6
  6  8  1  0
  8  9  1  0
  8 10  2  0
 10 11  1  0
 11 12  2  0
 11 13  1  0
 13 14  1  0
 14 15  1  0
 14 16  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
  7 22  1  0
  9 23  1  0
  9 24  1  0
  9 25  1  0
 10 26  1  0
 13 27  1  0
 13 28  1  0
 15 29  1  0
 15 30  1  0
 15 31  1  0
 16 32  1  0
 16 33  1  0
 16 34  1  0
M  END


  Mrv1652309092201572D          

 16 16  0  0  1  0            999 V2000
    3.4000    2.2150    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5875    2.3582    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3054    3.1335    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0572    1.7262    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2448    1.8695    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.1842    1.8695    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
    2.1434    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    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
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8245    0.8538    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4372    1.5246    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  6  0  0  0
  6  7  1  1  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 10  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  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>
NP0276016

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(=O)\C=C\[C@]1(O)C(C)=CC(=O)CC1(C)C

> <INCHI_IDENTIFIER>
InChI=1S/C13H18O3/c1-9-7-11(15)8-12(3,4)13(9,16)6-5-10(2)14/h5-7,16H,8H2,1-4H3/b6-5+/t13-/m0/s1

> <INCHI_KEY>
JJRYPZMXNLLZFH-GFUIURDCSA-N

> <FORMULA>
C13H18O3

> <MOLECULAR_WEIGHT>
222.284

> <EXACT_MASS>
222.12559444

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
34

> <JCHEM_AVERAGE_POLARIZABILITY>
24.132801902066063

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(4R)-4-hydroxy-3,5,5-trimethyl-4-[(1E)-3-oxobut-1-en-1-yl]cyclohex-2-en-1-one

> <JCHEM_LOGP>
1.6523240710000004

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
19.034527167005127

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.372685613937566

> <JCHEM_PKA_STRONGEST_BASIC>
-3.5105853036630945

> <JCHEM_POLAR_SURFACE_AREA>
54.37

> <JCHEM_REFRACTIVITY>
63.926899999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(-)-dehydrovomifoliol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 09-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   09-SEP-22         0                                  
HETATM    1  C   UNK     0       6.347   4.135   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.830   4.402   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       4.303   5.849   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       3.840   3.222   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.324   3.490   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       0.344   3.490   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -1.539   1.594   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -0.816   2.846   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                                                            
CONECT    8    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   32    0
END

View in JSmol

Synonyms

Value	Source
(-)-Dehydrovomifoliol	ChEBI
(4R)-4-Hydroxy-3,5,5-trimethyl-4-[(1E)-3-oxobut-1-en-1-yl]cyclohex-2-en-1-one	ChEBI

Chemical Formula

C₁₃H₁₈O₃

Average Mass

222.2840 Da

Monoisotopic Mass

222.12559 Da

IUPAC Name

(4R)-4-hydroxy-3,5,5-trimethyl-4-[(1E)-3-oxobut-1-en-1-yl]cyclohex-2-en-1-one

Traditional Name

(-)-dehydrovomifoliol

CAS Registry Number

Not Available

SMILES

CC(=O)\C=C\[C@]1(O)C(C)=CC(=O)CC1(C)C

InChI Identifier

InChI=1S/C13H18O3/c1-9-7-11(15)8-12(3,4)13(9,16)6-5-10(2)14/h5-7,16H,8H2,1-4H3/b6-5+/t13-/m0/s1

InChI Key

JJRYPZMXNLLZFH-GFUIURDCSA-N

Experimental Spectra

Not Available

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

Not Available

Species

Species of Origin

Species Name	Source	Reference
Helianthus heterophyllus	LOTUS Database	35616633
Viburnum dilatatum	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as sesquiterpenoids. These are terpenes with three consecutive isoprene units.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Sesquiterpenoids

Direct Parent

Sesquiterpenoids

Alternative Parents

Substituents

Sesquiterpenoid
Megastigmane sesquiterpenoid
Cyclofarsesane sesquiterpenoid
Ionone derivative
Cyclohexenone
Acryloyl-group
Enone
Alpha,beta-unsaturated ketone
Tertiary alcohol
Ketone
Cyclic ketone
Organic oxide
Organic oxygen compound
Organooxygen compound
Alcohol
Hydrocarbon derivative
Carbonyl group
Aliphatic homomonocyclic compound

Molecular Framework

Aliphatic homomonocyclic compounds

External Descriptors

dehydrovomifoliol (CHEBI:49177 )

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	1.65	ChemAxon
pKa (Strongest Acidic)	13.37	ChemAxon
pKa (Strongest Basic)	-3.5	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	54.37 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	63.93 m³·mol⁻¹	ChemAxon
Polarizability	24.13 Å³	ChemAxon
Number of Rings	1	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

599942

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

688494

PDB ID

Not Available

ChEBI ID

49177

Good Scents ID

Not Available

References

General References

Zhang SL, Liao HB, Liang D: [Chemical constitutes from Clerodendrum japonicum]. Zhongguo Zhong Yao Za Zhi. 2018 Jul;43(13):2732-2739. doi: 10.19540/j.cnki.cjcmm.20180424.002. [PubMed:30111024 ]
LOTUS database [Link]

Showing NP-Card for (-)-dehydrovomifoliol (NP0276016)

MOL for NP0276016 ((-)-dehydrovomifoliol)

3D MOL for NP0276016 ((-)-dehydrovomifoliol)

3D SDF for NP0276016 ((-)-dehydrovomifoliol)

3D-SDF for NP0276016 ((-)-dehydrovomifoliol)

PDB for NP0276016 ((-)-dehydrovomifoliol)

3D PDB for NP0276016 ((-)-dehydrovomifoliol)

SMILES for NP0276016 ((-)-dehydrovomifoliol)

INCHI for NP0276016 ((-)-dehydrovomifoliol)

Structure for NP0276016 ((-)-dehydrovomifoliol)

3D Structure for NP0276016 ((-)-dehydrovomifoliol)