NP-MRD: Showing NP-Card for 3-Epinobilin (NP0048576)

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Record Information

Version

2.0

Created at

2022-03-17 20:58:38 UTC

Updated at

2022-03-17 20:58:38 UTC

NP-MRD ID

NP0048576

Secondary Accession Numbers

None

Natural Product Identification

Common Name

3-Epinobilin

Description

3-Epinobilin belongs to the class of organic compounds known as germacranolides and derivatives. These are sesquiterpene lactones with a structure based on the germacranolide skeleton, characterized by a gamma lactone fused to a 1,7-dimethylcyclodec-1-ene moiety. 3-Epinobilin is an extremely weak basic (essentially neutral) compound (based on its pKa). Outside of the human body, 3-Epinobilin has been detected, but not quantified in, herbs and spices and roman camomiles. 3-Epinobilin is found in Anthemis nobili. This could make 3-epinobilin a potential biomarker for the consumption of these foods.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652307301920062D          

 28 29  0  0  0  0            999 V2000
    2.2588   -2.3882    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2890    1.4129    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3186   -0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3328    3.2521    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8808    0.3310    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5501   -1.6163    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9012    1.3375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1925    2.1093    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7958    0.4320    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5643    1.8420    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0871    1.2038    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0273   -0.9781    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8556    2.6139    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3652    0.9751    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6697    2.7476    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9817    0.2983    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7502    1.7084    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4589    0.9365    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2132   -1.1117    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5832    1.7707    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9610    3.5194    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9219   -1.8836    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3551    2.0620    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6904   -0.4735    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1061    2.2240    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3642   -1.4826    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4240    0.6993    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3784    1.9757    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  6  1  1  0  0  0  0
  8  7  1  0  0  0  0
 11  2  1  0  0  0  0
 11  7  2  0  0  0  0
 11  9  1  0  0  0  0
 12  3  1  0  0  0  0
 12  6  2  0  0  0  0
 13  4  1  0  0  0  0
 13 10  2  0  0  0  0
 14  5  2  0  0  0  0
 15  8  1  0  0  0  0
 15 13  1  0  0  0  0
 16  9  1  0  0  0  0
 17 10  1  0  0  0  0
 18 14  1  0  0  0  0
 18 16  1  0  0  0  0
 18 17  1  0  0  0  0
 19 12  1  0  0  0  0
 20 14  1  0  0  0  0
 21 15  1  0  0  0  0
 22 19  2  0  0  0  0
 23 20  2  0  0  0  0
 24 16  1  0  0  0  0
 24 19  1  0  0  0  0
 25 17  1  0  0  0  0
 25 20  1  0  0  0  0
 26  6  1  0  0  0  0
 27  7  1  0  0  0  0
 28 10  1  0  0  0  0
M  END


  Mrv1652307301920062D          

 28 29  0  0  0  0            999 V2000
    2.2588   -2.3882    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2890    1.4129    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3186   -0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3328    3.2521    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8808    0.3310    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5501   -1.6163    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9012    1.3375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1925    2.1093    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7958    0.4320    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5643    1.8420    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0871    1.2038    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0273   -0.9781    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8556    2.6139    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3652    0.9751    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6697    2.7476    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9817    0.2983    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7502    1.7084    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4589    0.9365    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2132   -1.1117    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5832    1.7707    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9610    3.5194    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9219   -1.8836    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3551    2.0620    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6904   -0.4735    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1061    2.2240    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3642   -1.4826    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4240    0.6993    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3784    1.9757    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  6  1  1  0  0  0  0
  8  7  1  0  0  0  0
 11  2  1  0  0  0  0
 11  7  2  0  0  0  0
 11  9  1  0  0  0  0
 12  3  1  0  0  0  0
 12  6  2  0  0  0  0
 13  4  1  0  0  0  0
 13 10  2  0  0  0  0
 14  5  2  0  0  0  0
 15  8  1  0  0  0  0
 15 13  1  0  0  0  0
 16  9  1  0  0  0  0
 17 10  1  0  0  0  0
 18 14  1  0  0  0  0
 18 16  1  0  0  0  0
 18 17  1  0  0  0  0
 19 12  1  0  0  0  0
 20 14  1  0  0  0  0
 21 15  1  0  0  0  0
 22 19  2  0  0  0  0
 23 20  2  0  0  0  0
 24 16  1  0  0  0  0
 24 19  1  0  0  0  0
 25 17  1  0  0  0  0
 25 20  1  0  0  0  0
 26  6  1  0  0  0  0
 27  7  1  0  0  0  0
 28 10  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0048576

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]\C(C)=C(/C)C(=O)OC1C\C(C)=C([H])\CC(O)\C(C)=C([H])\C2OC(=O)C(=C)C12

> <INCHI_IDENTIFIER>
InChI=1S/C20H26O5/c1-6-12(3)19(22)24-16-9-11(2)7-8-15(21)13(4)10-17-18(16)14(5)20(23)25-17/h6-7,10,15-18,21H,5,8-9H2,1-4H3/b11-7+,12-6-,13-10+

> <INCHI_KEY>
QFINJHBXXJQKPB-QLDBJWRKSA-N

> <FORMULA>
C20H26O5

> <MOLECULAR_WEIGHT>
346.423

> <EXACT_MASS>
346.178023937

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
51

> <JCHEM_AVERAGE_POLARIZABILITY>
36.76327902475996

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
9-hydroxy-6,10-dimethyl-3-methylidene-2-oxo-2H,3H,3aH,4H,5H,8H,9H,11aH-cyclodeca[b]furan-4-yl (2Z)-2-methylbut-2-enoate

> <JCHEM_LOGP>
3.4531310143333336

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.554788584696674

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9935354730536687

> <JCHEM_POLAR_SURFACE_AREA>
72.83000000000001

> <JCHEM_REFRACTIVITY>
96.8624

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
9-hydroxy-6,10-dimethyl-3-methylidene-2-oxo-3aH,4H,5H,8H,9H,11aH-cyclodeca[b]furan-4-yl (2Z)-2-methylbut-2-enoate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 30-JUL-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   30-JUL-19         0                                  
HETATM    1  C   UNK     0       4.216  -4.458   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.406   2.637   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.328  -0.385   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.488   6.071   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -1.644   0.618   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.760  -3.017   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       5.416   2.497   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       5.959   3.937   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.352   0.806   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.920   3.438   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       3.896   2.247   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       3.784  -1.826   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       3.464   4.879   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -0.682   1.820   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       4.983   5.129   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       1.833   0.557   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       1.400   3.189   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       0.857   1.748   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       2.265  -2.075   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -1.089   3.305   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       5.527   6.570   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0       1.721  -3.516   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0      -2.530   3.849   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0       1.289  -0.884   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0       0.198   4.151   0.000  0.00  0.00           O+0
HETATM   26  H   UNK     0       6.280  -2.768   0.000  0.00  0.00           H+0
HETATM   27  H   UNK     0       6.391   1.305   0.000  0.00  0.00           H+0
HETATM   28  H   UNK     0       4.440   3.688   0.000  0.00  0.00           H+0
CONECT    1    6                                                            
CONECT    2   11                                                            
CONECT    3   12                                                            
CONECT    4   13                                                            
CONECT    5   14                                                            
CONECT    6    1   12   26                                                  
CONECT    7    8   11   27                                                  
CONECT    8    7   15                                                       
CONECT    9   11   16                                                       
CONECT   10   13   17   28                                                  
CONECT   11    2    7    9                                                  
CONECT   12    3    6   19                                                  
CONECT   13    4   10   15                                                  
CONECT   14    5   18   20                                                  
CONECT   15    8   13   21                                                  
CONECT   16    9   18   24                                                  
CONECT   17   10   18   25                                                  
CONECT   18   14   16   17                                                  
CONECT   19   12   22   24                                                  
CONECT   20   14   23   25                                                  
CONECT   21   15                                                            
CONECT   22   19                                                            
CONECT   23   20                                                            
CONECT   24   16   19                                                       
CONECT   25   17   20                                                       
CONECT   26    6                                                            
CONECT   27    7                                                            
CONECT   28   10                                                            
MASTER        0    0    0    0    0    0    0    0   28    0   58    0
END

View in JSmol

Synonyms

Value	Source
9-Hydroxy-6,10-dimethyl-3-methylidene-2-oxo-2H,3H,3ah,4H,5H,8H,9H,11ah-cyclodeca[b]furan-4-yl (2Z)-2-methylbut-2-enoic acid	Generator

Chemical Formula

C₂₀H₂₆O₅

Average Mass

346.4230 Da

Monoisotopic Mass

346.17802 Da

IUPAC Name

9-hydroxy-6,10-dimethyl-3-methylidene-2-oxo-2H,3H,3aH,4H,5H,8H,9H,11aH-cyclodeca[b]furan-4-yl (2Z)-2-methylbut-2-enoate

Traditional Name

9-hydroxy-6,10-dimethyl-3-methylidene-2-oxo-3aH,4H,5H,8H,9H,11aH-cyclodeca[b]furan-4-yl (2Z)-2-methylbut-2-enoate

CAS Registry Number

Not Available

SMILES

[H]\C(C)=C(/C)C(=O)OC1C\C(C)=C([H])\CC(O)\C(C)=C([H])\C2OC(=O)C(=C)C12

InChI Identifier

InChI=1S/C20H26O5/c1-6-12(3)19(22)24-16-9-11(2)7-8-15(21)13(4)10-17-18(16)14(5)20(23)25-17/h6-7,10,15-18,21H,5,8-9H2,1-4H3/b11-7+,12-6-,13-10+

InChI Key

QFINJHBXXJQKPB-QLDBJWRKSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Anthemis nobili	Plant	KNApSAcK
Chamaemelum nobile	FooDB	Dr. Duke's Phytochemical and Ethnobotanical Databases

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as germacranolides and derivatives. These are sesquiterpene lactones with a structure based on the germacranolide skeleton, characterized by a gamma lactone fused to a 1,7-dimethylcyclodec-1-ene moiety.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Terpene lactones

Direct Parent

Germacranolides and derivatives

Alternative Parents

Substituents

Germacranolide
Germacrane sesquiterpenoid
Sesquiterpenoid
Fatty acid ester
Dicarboxylic acid or derivatives
Gamma butyrolactone
Fatty acyl
Alpha,beta-unsaturated carboxylic ester
Tetrahydrofuran
Enoate ester
Secondary alcohol
Lactone
Carboxylic acid ester
Organoheterocyclic compound
Oxacycle
Carboxylic acid derivative
Organooxygen compound
Hydrocarbon derivative
Organic oxide
Organic oxygen compound
Alcohol
Carbonyl group
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	3.45	ChemAxon
pKa (Strongest Acidic)	14.55	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	72.83 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	96.86 m³·mol⁻¹	ChemAxon
Polarizability	36.76 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

HMDB0036690

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB015621

KNApSAcK ID

C00003339

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

131752037

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Showing NP-Card for 3-Epinobilin (NP0048576)

MOL for NP0048576 (3-Epinobilin)

3D MOL for NP0048576 (3-Epinobilin)

3D SDF for NP0048576 (3-Epinobilin)

3D-SDF for NP0048576 (3-Epinobilin)

PDB for NP0048576 (3-Epinobilin)

3D PDB for NP0048576 (3-Epinobilin)

SMILES for NP0048576 (3-Epinobilin)

INCHI for NP0048576 (3-Epinobilin)

Structure for NP0048576 (3-Epinobilin)

3D Structure for NP0048576 (3-Epinobilin)