NP-MRD: Showing NP-Card for Cyclobisuberodiene (NP0084802)

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Record Information

Version

2.0

Created at

2022-04-29 05:26:48 UTC

Updated at

2022-04-29 05:26:48 UTC

NP-MRD ID

NP0084802

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Cyclobisuberodiene

Description

Thamnosin belongs to the class of organic compounds known as coumarins and derivatives. These are polycyclic aromatic compounds containing a 1-benzopyran moiety with a ketone group at the C2 carbon atom (1-benzopyran-2-one). Thamnosin is an extremely weak basic (essentially neutral) compound (based on its pKa). Outside of the human body, Thamnosin has been detected, but not quantified in, citrus. Cyclobisuberodiene is found in Citrus grandis and Thamnosma montana. This could make thamnosin a potential biomarker for the consumption of these foods.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv0541 05061305202D          

 36 40  0  0  0  0            999 V2000
    6.4302   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4744    0.6817    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1922    1.7435    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0312    5.0467    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
    4.7491    5.8219    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
    5.7158    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5350    2.2322    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0047    1.6002    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7831    3.6395    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END

     RDKit          3D

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M  END


  Mrv0541 05061305202D          

 36 40  0  0  0  0            999 V2000
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    5.0013   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
> <DATABASE_ID>
NP0084802

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=CC2=C(C=CC(=O)O2)C=C1\C=C\C1(C)CCC(C)=CC1C1=C(OC)C=C2OC(=O)C=CC2=C1

> <INCHI_IDENTIFIER>
InChI=1S/C30H28O6/c1-18-9-11-30(2,12-10-21-14-19-5-7-28(31)35-25(19)16-24(21)33-3)23(13-18)22-15-20-6-8-29(32)36-26(20)17-27(22)34-4/h5-8,10,12-17,23H,9,11H2,1-4H3/b12-10+

> <INCHI_KEY>
SWGAQLQAABDHGT-ZRDIBKRKSA-N

> <FORMULA>
C30H28O6

> <MOLECULAR_WEIGHT>
484.5397

> <EXACT_MASS>
484.188588628

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
53.02656031688646

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
7-methoxy-6-{6-[(E)-2-(7-methoxy-2-oxo-2H-chromen-6-yl)ethenyl]-3,6-dimethylcyclohex-2-en-1-yl}-2H-chromen-2-one

> <ALOGPS_LOGP>
5.56

> <JCHEM_LOGP>
5.605345603666667

> <ALOGPS_LOGS>
-6.45

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-4.543395156085

> <JCHEM_POLAR_SURFACE_AREA>
71.06000000000002

> <JCHEM_REFRACTIVITY>
140.99309999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.70e-04 g/l

> <JCHEM_TRADITIONAL_IUPAC>
7-methoxy-6-{6-[(E)-2-(7-methoxy-2-oxochromen-6-yl)ethenyl]-3,6-dimethylcyclohex-2-en-1-yl}chromen-2-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 06-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAY-13         0                                  
HETATM    1  C   UNK     0      12.003  -0.770   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       6.486   1.273   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.959   3.255   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       9.336  -2.310   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       9.392   9.421   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       8.865  10.868   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      10.669   1.540   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       8.465   4.167   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       9.336   2.310   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       7.475   2.987   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       9.336  -0.770   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       8.928   6.794   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       5.895   7.329   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      10.669   0.000   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       8.402   8.241   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       7.939   5.614   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       8.002   0.000   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       6.422   5.881   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       6.885   8.508   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       6.668  -2.310   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       7.348  11.135   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       8.002   1.540   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0       6.822  12.582   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0       0.000  -3.080   0.000  0.00  0.00           O+0
HETATM   33  O   UNK     0       5.432   4.702   0.000  0.00  0.00           O+0
HETATM   34  O   UNK     0       8.002  -3.080   0.000  0.00  0.00           O+0
HETATM   35  O   UNK     0       6.358   9.955   0.000  0.00  0.00           O+0
HETATM   36  O   UNK     0       2.667  -3.080   0.000  0.00  0.00           O+0
CONECT    1   18                                                            
CONECT    2   30                                                            
CONECT    3   33                                                            
CONECT    4   34                                                            
CONECT    5    7   19                                                       
CONECT    6    8   20                                                       
CONECT    7    5   28                                                       
CONECT    8    6   29                                                       
CONECT    9   11   18                                                       
CONECT   10   12   21                                                       
CONECT   11    9   30                                                       
CONECT   12   10   30                                                       
CONECT   13   18   23                                                       
CONECT   14   19   21                                                       
CONECT   15   20   22                                                       
CONECT   16   24   25                                                       
CONECT   17   26   27                                                       
CONECT   18    1    9   13                                                  
CONECT   19    5   14   25                                                  
CONECT   20    6   15   26                                                  
CONECT   21   10   14   24                                                  
CONECT   22   15   23   27                                                  
CONECT   23   13   22   30                                                  
CONECT   24   16   21   33                                                  
CONECT   25   16   19   35                                                  
CONECT   26   17   20   36                                                  
CONECT   27   17   22   34                                                  
CONECT   28    7   31   35                                                  
CONECT   29    8   32   36                                                  
CONECT   30    2   11   12   23                                             
CONECT   31   28                                                            
CONECT   32   29                                                            
CONECT   33    3   24                                                       
CONECT   34    4   27                                                       
CONECT   35   25   28                                                       
CONECT   36   26   29                                                       
MASTER        0    0    0    0    0    0    0    0   36    0   80    0
END

View in JSmol

Synonyms

Value	Source
7-Methoxy-6-[2-[2-(7-methoxy-2-oxo-2H-1-benzopyran-6-yl)-1,4-dimethyl-3-cyclohexen-1-yl]ethenyl]-2H-1-benzopyran-2-one, 9ci	HMDB
Cyclobisuberodiene	HMDB

Chemical Formula

C₃₀H₂₈O₆

Average Mass

484.5397 Da

Monoisotopic Mass

484.18859 Da

IUPAC Name

7-methoxy-6-{6-[(E)-2-(7-methoxy-2-oxo-2H-chromen-6-yl)ethenyl]-3,6-dimethylcyclohex-2-en-1-yl}-2H-chromen-2-one

Traditional Name

7-methoxy-6-{6-[(E)-2-(7-methoxy-2-oxochromen-6-yl)ethenyl]-3,6-dimethylcyclohex-2-en-1-yl}chromen-2-one

CAS Registry Number

Not Available

SMILES

COC1=CC2=C(C=CC(=O)O2)C=C1\C=C\C1(C)CCC(C)=CC1C1=C(OC)C=C2OC(=O)C=CC2=C1

InChI Identifier

InChI=1S/C30H28O6/c1-18-9-11-30(2,12-10-21-14-19-5-7-28(31)35-25(19)16-24(21)33-3)23(13-18)22-15-20-6-8-29(32)36-26(20)17-27(22)34-4/h5-8,10,12-17,23H,9,11H2,1-4H3/b12-10+

InChI Key

SWGAQLQAABDHGT-ZRDIBKRKSA-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, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, 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
Citrus maxima	Plant	KNApSAcK
Thamnosma montana	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as coumarins and derivatives. These are polycyclic aromatic compounds containing a 1-benzopyran moiety with a ketone group at the C2 carbon atom (1-benzopyran-2-one).

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Coumarins and derivatives

Sub Class

Not Available

Direct Parent

Coumarins and derivatives

Alternative Parents

Substituents

Coumarin
Benzopyran
1-benzopyran
Anisole
Styrene
Alkyl aryl ether
Pyranone
Pyran
Benzenoid
Heteroaromatic compound
Lactone
Oxacycle
Ether
Organoheterocyclic compound
Organic oxygen compound
Organooxygen compound
Hydrocarbon derivative
Organic oxide
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
logP	5.56	ALOGPS
logP	5.61	ChemAxon
logS	-6.4	ALOGPS
pKa (Strongest Basic)	-4.5	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	71.06 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	140.99 m³·mol⁻¹	ChemAxon
Polarizability	53.03 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

HMDB0030550

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB002425

KNApSAcK ID

Not Available

Chemspider ID

4526172

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5377043

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Cyclobisuberodiene (NP0084802)

MOL for NP0084802 (Cyclobisuberodiene)

3D MOL for NP0084802 (Cyclobisuberodiene)

3D SDF for NP0084802 (Cyclobisuberodiene)

3D-SDF for NP0084802 (Cyclobisuberodiene)

PDB for NP0084802 (Cyclobisuberodiene)

3D PDB for NP0084802 (Cyclobisuberodiene)

SMILES for NP0084802 (Cyclobisuberodiene)

INCHI for NP0084802 (Cyclobisuberodiene)

Structure for NP0084802 (Cyclobisuberodiene)

3D Structure for NP0084802 (Cyclobisuberodiene)