NP-MRD: Showing NP-Card for (1s,4z,9s)-1-methyl-6-methylidene-10-oxabicyclo[7.1.0]dec-4-ene (NP0313001)

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Record Information

Version

2.0

Created at

2022-09-11 10:15:30 UTC

Updated at

2022-09-11 10:15:30 UTC

NP-MRD ID

NP0313001

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1s,4z,9s)-1-methyl-6-methylidene-10-oxabicyclo[7.1.0]dec-4-ene

Description

Xeniolide belongs to the class of organic compounds known as epoxides. Epoxides are compounds containing a cyclic ether with three ring atoms(one oxygen and two carbon atoms). (1s,4z,9s)-1-methyl-6-methylidene-10-oxabicyclo[7.1.0]dec-4-ene is found in Paragorgia arborea. (1s,4z,9s)-1-methyl-6-methylidene-10-oxabicyclo[7.1.0]dec-4-ene was first documented in 2009 (PMID: 19863101). Based on a literature review a small amount of articles have been published on Xeniolide (PMID: 33669051) (PMID: 28691521) (PMID: 33804495) (PMID: 31364881).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 28 29  0  0  0  0  0  0  0  0999 V2000
    2.9810   -0.1779    1.3494 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0985   -0.1597    0.3227 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7443   -1.4082   -0.2840 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5442   -1.9461   -0.2654 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6523   -1.4273    0.3530 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8037   -1.1201   -0.6210 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7849    0.3922   -0.6821 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.6287    1.0300    0.3810 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5593    1.1418   -1.7841 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4717    0.7801   -1.0527 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.2574    1.5612   -0.0494 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7104    1.2093   -0.0689 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3919   -1.0938    1.6846 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2768    0.7501    1.8378 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5732   -2.0026   -0.8057 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4362   -2.9236   -0.7987 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0868   -2.2983    0.9618 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5459   -0.6348    1.0824 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4866   -1.5214   -1.6005 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7662   -1.4882   -0.2620 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3794    2.0587    0.6164 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6845    1.0262   -0.0014 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6458    0.4483    1.3327 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1635    0.0395   -1.6305 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2332    2.6498   -0.4174 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1816    1.6505    0.9619 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2185    1.9918    0.5506 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0484    1.4726   -1.1103 H   0  0  0  0  0  0  0  0  0  0  0  0
  7  8  1  1
  7  6  1  0
  6  5  1  0
  5  4  1  0
  4  3  2  0
  3  2  1  0
  2  1  2  0
  2 12  1  0
 12 11  1  0
 11 10  1  0
 10  9  1  0
 10  7  1  0
  9  7  1  0
  8 21  1  0
  8 22  1  0
  8 23  1  0
  6 19  1  0
  6 20  1  0
  5 17  1  0
  5 18  1  0
  4 16  1  0
  3 15  1  0
  1 13  1  0
  1 14  1  0
 12 27  1  0
 12 28  1  0
 11 25  1  0
 11 26  1  0
 10 24  1  6
M  END

HEADER    PROTEIN                                 11-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-22         0                                  
HETATM    1  C   UNK     0       9.986   4.083   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       8.806   3.093   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       9.333   1.646   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       8.806   0.198   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       7.472  -0.572   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       5.956  -0.304   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.966   0.876   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       3.976  -0.304   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       3.632   1.646   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       4.966   2.416   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       5.956   3.595   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       7.472   3.863   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   12                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8    9   10                                             
CONECT    8    7                                                            
CONECT    9    7   10                                                       
CONECT   10    9    7   11                                                  
CONECT   11   10   12                                                       
CONECT   12   11    2                                                       
MASTER        0    0    0    0    0    0    0    0   12    0   26    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₁H₁₆O

Average Mass

164.2480 Da

Monoisotopic Mass

164.12012 Da

IUPAC Name

(1S,4Z,9S)-1-methyl-6-methylidene-10-oxabicyclo[7.1.0]dec-4-ene

Traditional Name

(1S,4Z,9S)-1-methyl-6-methylidene-10-oxabicyclo[7.1.0]dec-4-ene

CAS Registry Number

Not Available

SMILES

C[C@]12CC\C=C/C(=C)CC[C@@H]1O2

InChI Identifier

InChI=1S/C11H16O/c1-9-5-3-4-8-11(2)10(12-11)7-6-9/h3,5,10H,1,4,6-8H2,2H3/b5-3-/t10-,11-/m0/s1

InChI Key

GVWMTRPEBKLXPR-NBLPHYOQSA-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
Paragorgia arborea	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as epoxides. Epoxides are compounds containing a cyclic ether with three ring atoms(one oxygen and two carbon atoms).

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Epoxides

Sub Class

Not Available

Direct Parent

Epoxides

Alternative Parents

Substituents

Oxacycle
Ether
Oxirane
Dialkyl ether
Organic oxygen compound
Hydrocarbon derivative
Organooxygen compound
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	2.56	ChemAxon
pKa (Strongest Basic)	-4.2	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	1	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	12.53 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	51.01 m³·mol⁻¹	ChemAxon
Polarizability	18.64 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	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

C00041242

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

51350596

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Lin YC, Chen YJ, Chen SR, Lien WJ, Chang HW, Yang YL, Liaw CC, Su JH, Chen CY, Cheng YB: Targeted Isolation of Xenicane Diterpenoids from Taiwanese Soft Coral Asterospicularia laurae. Mar Drugs. 2021 Feb 25;19(3). pii: md19030123. doi: 10.3390/md19030123. [PubMed:33669051 ]
Phan CS, Kamada T, Kobayashi K, Hamada T, Vairappan CS: 15-deoxy-isoxeniolide-A, new diterpenoid from a bornean soft coral, Xenia sp. Nat Prod Res. 2018 Jan;32(2):202-207. doi: 10.1080/14786419.2017.1346638. Epub 2017 Jul 10. [PubMed:28691521 ]
Lin YC, Abd El-Razek MH, Hwang TL, Chiang MY, Kuo YH, Dai CF, Shen YC: Asterolaurins A-F, xenicane diterpenoids from the Taiwanese soft coral Asterospicularia laurae. J Nat Prod. 2009 Nov;72(11):1911-6. doi: 10.1021/np900231e. [PubMed:19863101 ]
Althagbi HI, Budiyanto F, Abdel-Lateff A, Al-Footy KO, Bawakid NO, Ghandourah MA, Alfaifi MY, Elbehairi SEI, Alarif WM: Antiproliferative Isoprenoid Derivatives from the Red Sea Alcyonacean Xenia umbellata. Molecules. 2021 Mar 1;26(5):1311. doi: 10.3390/molecules26051311. [PubMed:33804495 ]
Su JH, Liu CI, Lu MC, Chang CI, Hsieh MY, Lin YC, Dai CF, Zhang YH, Lin ZY, Lin YS: New secondary metabolite with cytotoxicity from spawning soft coral Asterospicularia laurae in Taiwan. Nat Prod Res. 2021 Mar;35(6):967-975. doi: 10.1080/14786419.2019.1614579. Epub 2019 Jul 31. [PubMed:31364881 ]
LOTUS database [Link]

Showing NP-Card for (1s,4z,9s)-1-methyl-6-methylidene-10-oxabicyclo[7.1.0]dec-4-ene (NP0313001)

MOL for NP0313001 ((1s,4z,9s)-1-methyl-6-methylidene-10-oxabicyclo[7.1.0]dec-4-ene)

3D MOL for NP0313001 ((1s,4z,9s)-1-methyl-6-methylidene-10-oxabicyclo[7.1.0]dec-4-ene)

3D SDF for NP0313001 ((1s,4z,9s)-1-methyl-6-methylidene-10-oxabicyclo[7.1.0]dec-4-ene)

3D-SDF for NP0313001 ((1s,4z,9s)-1-methyl-6-methylidene-10-oxabicyclo[7.1.0]dec-4-ene)

PDB for NP0313001 ((1s,4z,9s)-1-methyl-6-methylidene-10-oxabicyclo[7.1.0]dec-4-ene)

3D PDB for NP0313001 ((1s,4z,9s)-1-methyl-6-methylidene-10-oxabicyclo[7.1.0]dec-4-ene)

SMILES for NP0313001 ((1s,4z,9s)-1-methyl-6-methylidene-10-oxabicyclo[7.1.0]dec-4-ene)

INCHI for NP0313001 ((1s,4z,9s)-1-methyl-6-methylidene-10-oxabicyclo[7.1.0]dec-4-ene)

Structure for NP0313001 ((1s,4z,9s)-1-methyl-6-methylidene-10-oxabicyclo[7.1.0]dec-4-ene)

3D Structure for NP0313001 ((1s,4z,9s)-1-methyl-6-methylidene-10-oxabicyclo[7.1.0]dec-4-ene)