NP-MRD: Showing NP-Card for (3r,5s,8e)-5,9,14-trimethyl-4,12-dioxatricyclo[9.3.0.0³,⁵]tetradeca-1(11),8,13-trien-2-one (NP0243006)

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Record Information

Version

2.0

Created at

2022-09-07 03:27:54 UTC

Updated at

2022-09-07 03:27:54 UTC

NP-MRD ID

NP0243006

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(3r,5s,8e)-5,9,14-trimethyl-4,12-dioxatricyclo[9.3.0.0³,⁵]tetradeca-1(11),8,13-trien-2-one

Description

Zederone belongs to the class of organic compounds known as germacrane sesquiterpenoids. These are sesquiterpenoids having the germacrane skeleton, with a structure characterized by a cyclodecane ring substituted with an isopropyl and two methyl groups. (3r,5s,8e)-5,9,14-trimethyl-4,12-dioxatricyclo[9.3.0.0³,⁵]tetradeca-1(11),8,13-trien-2-one is found in Curcuma longa. (3r,5s,8e)-5,9,14-trimethyl-4,12-dioxatricyclo[9.3.0.0³,⁵]tetradeca-1(11),8,13-trien-2-one was first documented in 2021 (PMID: 34539848). Based on a literature review a small amount of articles have been published on Zederone (PMID: 35658750) (PMID: 36017755) (PMID: 34455974) (PMID: 34402285).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 36 38  0  0  0  0  0  0  0  0999 V2000
   -0.0496    2.6917    1.2189 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5803    1.9569    0.0582 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8886    1.7838   -0.0060 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5997    1.0792   -1.0996 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8479   -0.3787   -0.7659 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5900   -1.0589   -0.2728 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.3472   -1.0749    1.1956 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5412   -2.4647   -0.7626 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7139   -1.4090   -1.2878 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7184   -1.6062   -1.0243 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2174   -2.7021   -1.4552 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5883   -0.6687   -0.3263 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7155   -0.9413    0.4354 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3255   -2.2629    0.7342 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2129    0.2830    0.9002 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4258    1.2211    0.4397 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4488    0.6851   -0.2944 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3776    1.4651   -0.9687 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7123    3.4447    0.7841 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7621    3.1866    1.7924 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5937    1.9375    1.8394 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4891    2.1871    0.8018 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6216    1.5271   -1.2637 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0904    1.1721   -2.0815 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6312   -0.4838   -0.0098 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2101   -0.8561   -1.7121 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9404   -1.9042    1.6442 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6707   -0.1549    1.7194 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2779   -1.3182    1.4124 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9584   -1.2468   -2.3510 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1883   -2.9798   -0.1054 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4243   -2.1009    0.8527 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9278   -2.7173    1.6525 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0959    0.4034    1.5288 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8016    2.4018   -1.4402 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0632    0.9034   -1.7826 H   0  0  0  0  0  0  0  0  0  0  0  0
 14 13  1  0
 13 15  2  0
 15 16  1  0
 16 17  1  0
 17 12  2  0
 12 10  1  0
 10 11  2  0
 10  9  1  0
  9  8  1  0
  8  6  1  0
  6  7  1  1
  6  5  1  0
  5  4  1  0
  4  3  1  0
  3  2  2  0
  2  1  1  0
  2 18  1  0
 12 13  1  0
  6  9  1  0
 18 17  1  0
 14 31  1  0
 14 32  1  0
 14 33  1  0
 15 34  1  0
  9 30  1  6
  7 27  1  0
  7 28  1  0
  7 29  1  0
  5 25  1  0
  5 26  1  0
  4 23  1  0
  4 24  1  0
  3 22  1  0
  1 19  1  0
  1 20  1  0
  1 21  1  0
 18 35  1  0
 18 36  1  0
M  END


  Mrv1652309072205272D          

 18 20  0  0  1  0            999 V2000
    3.7292    4.1948    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6373    3.3749    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3013    2.8854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0573    3.2157    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7214    2.7262    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6295    1.9063    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.4493    1.8144    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5376    1.0865    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8735    1.5760    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.2094    2.0655    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8019    2.7828    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4534    1.7352    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1931    0.9523    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6734    0.2816    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3681    0.9580    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1186    1.7444    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7894    2.2247    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8813    3.0446    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
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  1  0  0  0
  6  8  1  0  0  0  0
  9  8  1  1  0  0  0
  6  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 10 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 13 15  2  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 12 17  2  0  0  0  0
 17 18  1  0  0  0  0
  2 18  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0243006

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC1=COC2=C1C(=O)[C@@H]1O[C@@]1(C)CC\C=C(C)\C2

> <INCHI_IDENTIFIER>
InChI=1S/C15H18O3/c1-9-5-4-6-15(3)14(18-15)13(16)12-10(2)8-17-11(12)7-9/h5,8,14H,4,6-7H2,1-3H3/b9-5+/t14-,15-/m0/s1

> <INCHI_KEY>
CVIVANCKIBYAOP-WSQYCBKMSA-N

> <FORMULA>
C15H18O3

> <MOLECULAR_WEIGHT>
246.306

> <EXACT_MASS>
246.12559444

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
36

> <JCHEM_AVERAGE_POLARIZABILITY>
26.40660317744211

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(3R,5S,8E)-5,9,14-trimethyl-4,12-dioxatricyclo[9.3.0.0^{3,5}]tetradeca-1(11),8,13-trien-2-one

> <JCHEM_LOGP>
2.8549102296666664

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
15.140601825073734

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9377951159073348

> <JCHEM_POLAR_SURFACE_AREA>
42.74

> <JCHEM_REFRACTIVITY>
69.69720000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(3R,5S,8E)-5,9,14-trimethyl-4,12-dioxatricyclo[9.3.0.0^{3,5}]tetradeca-1(11),8,13-trien-2-one

> <JCHEM_VEBER_RULE>
0

$$$$

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  C   UNK     0       6.961   7.830   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       6.790   6.300   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       8.029   5.386   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       9.440   6.003   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      10.680   5.089   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      10.508   3.559   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      12.039   3.387   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      10.337   2.028   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       9.097   2.942   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       7.858   3.856   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       7.097   5.195   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       6.446   3.239   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.960   1.778   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       6.857   0.526   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       4.420   1.788   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       3.955   3.256   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       5.207   4.153   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       5.378   5.683   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   18                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7    8    9                                             
CONECT    7    6                                                            
CONECT    8    6    9                                                       
CONECT    9    8    6   10                                                  
CONECT   10    9   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13   17                                                  
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   12   18                                                  
CONECT   18   17    2                                                       
MASTER        0    0    0    0    0    0    0    0   18    0   40    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₅H₁₈O₃

Average Mass

246.3060 Da

Monoisotopic Mass

246.12559 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

CC1=COC2=C1C(=O)[C@@H]1O[C@@]1(C)CC\C=C(C)\C2

InChI Identifier

InChI=1S/C15H18O3/c1-9-5-4-6-15(3)14(18-15)13(16)12-10(2)8-17-11(12)7-9/h5,8,14H,4,6-7H2,1-3H3/b9-5+/t14-,15-/m0/s1

InChI Key

CVIVANCKIBYAOP-WSQYCBKMSA-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
Curcuma longa	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as germacrane sesquiterpenoids. These are sesquiterpenoids having the germacrane skeleton, with a structure characterized by a cyclodecane ring substituted with an isopropyl and two methyl groups.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Sesquiterpenoids

Direct Parent

Germacrane sesquiterpenoids

Alternative Parents

Substituents

Germacrane sesquiterpenoid
Aryl ketone
Aryl alkyl ketone
Furan
Heteroaromatic compound
Ketone
Organoheterocyclic compound
Ether
Oxirane
Oxacycle
Dialkyl ether
Hydrocarbon derivative
Organic oxide
Organooxygen compound
Organic oxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic 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

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00012324

Chemspider ID

23199370

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

71694446

PDB ID

Not Available

ChEBI ID

182234

Good Scents ID

Not Available

References

General References

Al-Amin M, Eltayeb NM, Hossain CF, Rahiman SSF, Khairuddean M, Muhamad Salhimi S: Bioactive compounds from Curcuma aeruginosa and the effect of comosone II on the migration and invasion of breast cancer cells. J Asian Nat Prod Res. 2022 Jun 4:1-12. doi: 10.1080/10286020.2022.2081562. [PubMed:35658750 ]
Qin Y, Fei C, Zhang W, Su L, Ji D, Bian Z, Wang M, Li Y, Mao C, Zhao X, Lu T: Based on UPLC/MS/MS and Bioinformatics Analysis to Explore the Difference Substances and Mechanism of Curcumae Radix (Curcuma wenyujin) in Dysmenorrhea. Chem Biodivers. 2022 Oct;19(10):e202200361. doi: 10.1002/cbdv.202200361. Epub 2022 Sep 16. [PubMed:36017755 ]
Yang X, Guan Y, Yan B, Xie Y, Zhou M, Wu Y, Yao L, Qiu X, Yan F, Chen Y, Huang L: Evidence-based complementary and alternative medicine bioinformatics approach through network pharmacology and molecular docking to determine the molecular mechanisms of Erjing pill in Alzheimer's disease. Exp Ther Med. 2021 Nov;22(5):1252. doi: 10.3892/etm.2021.10687. Epub 2021 Sep 2. [PubMed:34539848 ]
Borah S, Sarkar P, Sharma HK: Zederone Improves the Fecal Microbial Profile in Dementia Induced Rat Model: A First Report. CNS Neurol Disord Drug Targets. 2022;21(4):335-342. doi: 10.2174/1871527320666210827114227. [PubMed:34455974 ]
Lan ZW, Wang LH, Li QT, Wang SM, Meng J: [Analysis of volatile oil components of different species of Curcumae Rhizoma based on GC-MS and chemometrics]. Zhongguo Zhong Yao Za Zhi. 2021 Jul;46(14):3614-3624. doi: 10.19540/j.cnki.cjcmm.20210304.202. [PubMed:34402285 ]
LOTUS database [Link]

Showing NP-Card for (3r,5s,8e)-5,9,14-trimethyl-4,12-dioxatricyclo[9.3.0.0³,⁵]tetradeca-1(11),8,13-trien-2-one (NP0243006)

MOL for NP0243006 ((3r,5s,8e)-5,9,14-trimethyl-4,12-dioxatricyclo[9.3.0.0³,⁵]tetradeca-1(11),8,13-trien-2-one)

3D MOL for NP0243006 ((3r,5s,8e)-5,9,14-trimethyl-4,12-dioxatricyclo[9.3.0.0³,⁵]tetradeca-1(11),8,13-trien-2-one)

3D SDF for NP0243006 ((3r,5s,8e)-5,9,14-trimethyl-4,12-dioxatricyclo[9.3.0.0³,⁵]tetradeca-1(11),8,13-trien-2-one)

3D-SDF for NP0243006 ((3r,5s,8e)-5,9,14-trimethyl-4,12-dioxatricyclo[9.3.0.0³,⁵]tetradeca-1(11),8,13-trien-2-one)

PDB for NP0243006 ((3r,5s,8e)-5,9,14-trimethyl-4,12-dioxatricyclo[9.3.0.0³,⁵]tetradeca-1(11),8,13-trien-2-one)

3D PDB for NP0243006 ((3r,5s,8e)-5,9,14-trimethyl-4,12-dioxatricyclo[9.3.0.0³,⁵]tetradeca-1(11),8,13-trien-2-one)

SMILES for NP0243006 ((3r,5s,8e)-5,9,14-trimethyl-4,12-dioxatricyclo[9.3.0.0³,⁵]tetradeca-1(11),8,13-trien-2-one)

INCHI for NP0243006 ((3r,5s,8e)-5,9,14-trimethyl-4,12-dioxatricyclo[9.3.0.0³,⁵]tetradeca-1(11),8,13-trien-2-one)

Structure for NP0243006 ((3r,5s,8e)-5,9,14-trimethyl-4,12-dioxatricyclo[9.3.0.0³,⁵]tetradeca-1(11),8,13-trien-2-one)

3D Structure for NP0243006 ((3r,5s,8e)-5,9,14-trimethyl-4,12-dioxatricyclo[9.3.0.0³,⁵]tetradeca-1(11),8,13-trien-2-one)