MiMeDB: Showing metabocard for Clavaphyllene (MMDBc0002764)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-05-14 21:01:17 UTC

Update Date

2022-08-31 06:19:48 UTC

Metabolite ID

MMDBc0002764

Metabolite Identification

Common Name

Clavaphyllene

Description

(1R,9S,11R)-11-(4,8-dimethylnona-3,7-dien-1-yl)-4,11-dimethyl-8-methylidenebicyclo[7.2.0]undec-4-ene belongs to the class of organic compounds known as xeniaphyllane and xenicane diterpenoids. These are diterpenoids with a structure based either on the xeniaphyllane or the xenicane skeleton. Based on a literature review very few articles have been published on (1R,9S,11R)-11-(4,8-dimethylnona-3,7-dien-1-yl)-4,11-dimethyl-8-methylidenebicyclo[7.2.0]undec-4-ene.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305142123012D          

 27 28  0  0  1  0            999 V2000
    2.9227    7.9387    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6372    6.7012    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2082    4.2262    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0080    3.0568    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4366   -0.0077    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6688    2.1637    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2082    5.8762    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3760    0.9760    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7793    3.4012    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2082    6.7012    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4938    5.4637    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6582    1.7512    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7793    4.2262    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6615    0.5635    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6615    2.9390    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8491    2.7957    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4938    2.9887    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4938    1.3387    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9227    7.1137    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4938    4.6387    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3760    2.5265    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8491    0.7067    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3188    1.3387    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.3188    2.1637    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.4938    2.1637    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.0940    1.6209    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9701    2.9114    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
 10  7  1  0  0  0  0
 11  7  1  0  0  0  0
 12  8  1  4  0  0  0
 13  9  1  4  0  0  0
 14  8  1  0  0  0  0
 16 15  1  0  0  0  0
 17  9  1  0  0  0  0
 19  1  1  0  0  0  0
 19  2  1  0  0  0  0
 19 10  2  0  0  0  0
 20  3  1  0  0  0  0
 20 11  1  0  0  0  0
 20 13  2  0  0  0  0
 21  4  1  0  0  0  0
 21 12  2  0  0  0  0
 21 15  1  0  0  0  0
 22  5  2  0  0  0  0
 22 14  1  0  0  0  0
 23 18  1  0  0  0  0
 23 22  1  0  0  0  0
 24 16  1  0  0  0  0
 24 23  1  0  0  0  0
 25  6  1  6  0  0  0
 25 17  1  1  0  0  0
 25 18  1  0  0  0  0
 25 24  1  0  0  0  0
 23 26  1  6  0  0  0
 24 27  1  1  0  0  0
M  END


  Mrv1652305142123012D          

 27 28  0  0  1  0            999 V2000
    2.9227    7.9387    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6372    6.7012    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2082    4.2262    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0080    3.0568    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4366   -0.0077    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6688    2.1637    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2082    5.8762    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3760    0.9760    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7793    3.4012    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2082    6.7012    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4938    5.4637    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6582    1.7512    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7793    4.2262    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6615    0.5635    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6615    2.9390    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8491    2.7957    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4938    2.9887    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4938    1.3387    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9227    7.1137    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4938    4.6387    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3760    2.5265    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8491    0.7067    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3188    1.3387    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.3188    2.1637    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.4938    2.1637    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.0940    1.6209    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9701    2.9114    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
 10  7  1  0  0  0  0
 11  7  1  0  0  0  0
 12  8  1  4  0  0  0
 13  9  1  4  0  0  0
 14  8  1  0  0  0  0
 16 15  1  0  0  0  0
 17  9  1  0  0  0  0
 19  1  1  0  0  0  0
 19  2  1  0  0  0  0
 19 10  2  0  0  0  0
 20  3  1  0  0  0  0
 20 11  1  0  0  0  0
 20 13  2  0  0  0  0
 21  4  1  0  0  0  0
 21 12  2  0  0  0  0
 21 15  1  0  0  0  0
 22  5  2  0  0  0  0
 22 14  1  0  0  0  0
 23 18  1  0  0  0  0
 23 22  1  0  0  0  0
 24 16  1  0  0  0  0
 24 23  1  0  0  0  0
 25  6  1  6  0  0  0
 25 17  1  1  0  0  0
 25 18  1  0  0  0  0
 25 24  1  0  0  0  0
 23 26  1  6  0  0  0
 24 27  1  1  0  0  0
M  END
> <DATABASE_ID>
MMDBc0002764

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@]12C[C@@](C)(CCC=C(C)CCC=C(C)C)[C@]1([H])CCC(C)=CCCC2=C

> <INCHI_IDENTIFIER>
InChI=1S/C25H40/c1-19(2)10-7-11-20(3)13-9-17-25(6)18-23-22(5)14-8-12-21(4)15-16-24(23)25/h10,12-13,23-24H,5,7-9,11,14-18H2,1-4,6H3/t23-,24-,25-/m1/s1

> <INCHI_KEY>
KEWHXPJNBRKPIV-UBFVSLLYSA-N

> <FORMULA>
C25H40

> <MOLECULAR_WEIGHT>
340.595

> <EXACT_MASS>
340.313001288

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_ATOM_COUNT>
65

> <JCHEM_AVERAGE_POLARIZABILITY>
44.330346432313405

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1R,9S,11R)-11-(4,8-dimethylnona-3,7-dien-1-yl)-4,11-dimethyl-8-methylidenebicyclo[7.2.0]undec-4-ene

> <ALOGPS_LOGP>
8.00

> <JCHEM_LOGP>
7.8387379416666665

> <ALOGPS_LOGS>
-5.97

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_POLAR_SURFACE_AREA>
0.0

> <JCHEM_REFRACTIVITY>
115.05759999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
3.65e-04 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1R,9S,11R)-11-(4,8-dimethylnona-3,7-dien-1-yl)-4,11-dimethyl-8-methylidenebicyclo[7.2.0]undec-4-ene

> <JCHEM_VEBER_RULE>
1

$$$$

HEADER    PROTEIN                                 14-MAY-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   14-MAY-21         0                                  
HETATM    1  C   UNK     0       5.456  14.819   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       6.789  12.509   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.122   7.889   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       9.348   5.706   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.548  -0.014   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.248   4.039   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.122  10.969   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       8.169   1.822   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.455   6.349   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.122  12.509   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.788  10.199   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       8.695   3.269   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       1.455   7.889   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       6.835   1.052   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       6.835   5.486   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       5.318   5.219   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       2.788   5.579   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       2.788   2.499   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       5.456  13.279   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       2.788   8.659   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       8.169   4.716   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       5.318   1.319   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       4.328   2.499   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       4.328   4.039   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       2.788   4.039   0.000  0.00  0.00           C+0
HETATM   26  H   UNK     0       5.775   3.026   0.000  0.00  0.00           H+0
HETATM   27  H   UNK     0       3.678   5.435   0.000  0.00  0.00           H+0
CONECT    1   19                                                            
CONECT    2   19                                                            
CONECT    3   20                                                            
CONECT    4   21                                                            
CONECT    5   22                                                            
CONECT    6   25                                                            
CONECT    7   10   11                                                       
CONECT    8   12   14                                                       
CONECT    9   13   17                                                       
CONECT   10    7   19                                                       
CONECT   11    7   20                                                       
CONECT   12    8   21                                                       
CONECT   13    9   20                                                       
CONECT   14    8   22                                                       
CONECT   15   16   21                                                       
CONECT   16   15   24                                                       
CONECT   17    9   25                                                       
CONECT   18   23   25                                                       
CONECT   19    1    2   10                                                  
CONECT   20    3   11   13                                                  
CONECT   21    4   12   15                                                  
CONECT   22    5   14   23                                                  
CONECT   23   18   22   24   26                                             
CONECT   24   16   23   25   27                                             
CONECT   25    6   17   18   24                                             
CONECT   26   23                                                            
CONECT   27   24                                                            
MASTER        0    0    0    0    0    0    0    0   27    0   56    0
END

Synonyms

Not Available

Molecular Formula

C₂₅H₄₀

Average Mass

340.595

Monoisotopic Mass

340.313001288

IUPAC Name

(1R,9S,11R)-11-(4,8-dimethylnona-3,7-dien-1-yl)-4,11-dimethyl-8-methylidenebicyclo[7.2.0]undec-4-ene

Traditional Name

(1R,9S,11R)-11-(4,8-dimethylnona-3,7-dien-1-yl)-4,11-dimethyl-8-methylidenebicyclo[7.2.0]undec-4-ene

CAS Registry Number

Not Available

SMILES

[H][C@]12C[C@@](C)(CCC=C(C)CCC=C(C)C)[C@]1([H])CCC(C)=CCCC2=C

InChI Identifier

InChI=1S/C25H40/c1-19(2)10-7-11-20(3)13-9-17-25(6)18-23-22(5)14-8-12-21(4)15-16-24(23)25/h10,12-13,23-24H,5,7-9,11,14-18H2,1-4,6H3/t23-,24-,25-/m1/s1

InChI Key

KEWHXPJNBRKPIV-UBFVSLLYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as xeniaphyllane and xenicane diterpenoids. These are diterpenoids with a structure based either on the xeniaphyllane or the xenicane skeleton.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Diterpenoids

Direct Parent

Xeniaphyllane and xenicane diterpenoids

Alternative Parents

Substituents

Xeniaphyllane diterpenoid
Branched unsaturated hydrocarbon
Polycyclic hydrocarbon
Cyclic olefin
Unsaturated aliphatic hydrocarbon
Unsaturated hydrocarbon
Olefin
Hydrocarbon
Aliphatic homopolycyclic compound

Molecular Framework

Aliphatic homopolycyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.00036 g/L	ALOGPS
logP	8	ALOGPS
logP	7.84	ChemAxon
logS	-6	ALOGPS
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	0	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	0 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	115.06 m³·mol⁻¹	ChemAxon
Polarizability	44.33 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	Not Available	2022-08-10	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-20	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Not Available

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Eukaryota/Fungi	Ascomycota	1	Human feces	Metabolic reconstruction

Exposure Sources

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

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

139583648

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

van Santen JA, Poynton EF, Iskakova D, McMann E, Alsup TA, Clark TN, Fergusson CH, Fewer DP, Hughes AH, McCadden CA, Parra J, Soldatou S, Rudolf JD, Janssen EM, Duncan KR, Linington RG: The Natural Products Atlas 2.0: a database of microbially-derived natural products. Nucleic Acids Res. 2022 Jan 7;50(D1):D1317-D1323. doi: 10.1093/nar/gkab941. [PubMed:34718710 ]

Showing metabocard for Clavaphyllene (MMDBc0002764)

MOL for #<Metabolite:0x00007fdb6e865ca8>

3D MOL for #<Metabolite:0x00007fdb6e865ca8>

3D SDF for #<Metabolite:0x00007fdb6e865ca8>

3D-SDF for #<Metabolite:0x00007fdb6e865ca8>

PDB for #<Metabolite:0x00007fdb6e865ca8>

3D PDB for #<Metabolite:0x00007fdb6e865ca8>

SMILES for #<Metabolite:0x00007fdb6e865ca8>

INCHI for #<Metabolite:0x00007fdb6e865ca8>

Structure for #<Metabolite:0x00007fdb6e865ca8>

3D Structure for #<Metabolite:0x00007fdb6e865ca8>