NP-MRD: Showing NP-Card for Bergapin (NP0331583)

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Record Information

Version

2.0

Created at

2023-04-15 00:12:33 UTC

Updated at

2024-09-03 04:16:11 UTC

NP-MRD ID

NP0331583

Natural Product DOI

https://doi.org/10.57994/0563

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Bergapin

Description

Bergapten, also known as O-methylbergaptol or pentaderm, belongs to the class of organic compounds known as 5-methoxypsoralens. These are psoralens containing a methoxy group attached at the C5 position of the psoralen group. Outside of the human body, Bergapten is found, on average, in the highest concentration within a few different foods, such as anises (Pimpinella anisum), figs (Ficus carica), and parsnips (Pastinaca sativa) and in a lower concentration in wild carrots (Daucus carota), wild celeries (Apium graveolens), and parsleys (Petroselinum crispum). Bergapten has also been detected, but not quantified in, several different foods, such as roman camomiles (Chamaemelum nobile), alpine sweetvetches (Hedysarum alpinum), sweet rowanberries (Grataegosorbus mitschurinii), teffs (Eragrostis tef), and kiwis (Actinidia chinensis). This could make bergapten a potential biomarker for the consumption of these foods. Bergapten is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. Bergapin was first documented in 2010 (PMID: 21273683). Based on a literature review a small amount of articles have been published on Bergapten (PMID: 20433072) (PMID: 22611312).

Structure

MOL SDF PDB SMILES InChI

Bergapten
  Mrv1652305201900042D          

 16 18  0  0  0  0            999 V2000
    2.6378    0.1271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523   -0.2854    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0668   -1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7812   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4957   -1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4957   -2.3479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2102   -2.7604    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7812   -2.7604    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0668   -2.3479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523   -2.7604    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378   -2.3479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378   -1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8532   -1.2680    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3683   -1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8532   -2.6029    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
  9 10  1  0  0  0  0
  4 10  1  0  0  0  0
 10 11  2  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
  3 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  2  0  0  0  0
 15 16  1  0  0  0  0
 12 16  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0331583

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=C2C=CC(=O)OC2=CC2=C1C=CO2

> <INCHI_IDENTIFIER>
InChI=1S/C12H8O4/c1-14-12-7-2-3-11(13)16-10(7)6-9-8(12)4-5-15-9/h2-6H,1H3

> <INCHI_KEY>
BGEBZHIAGXMEMV-UHFFFAOYSA-N

> <FORMULA>
C12H8O4

> <MOLECULAR_WEIGHT>
216.192

> <EXACT_MASS>
216.042258738

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
24

> <JCHEM_AVERAGE_POLARIZABILITY>
20.8726120878251

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
4-methoxy-7H-furo[3,2-g]chromen-7-one

> <ALOGPS_LOGP>
2.12

> <JCHEM_LOGP>
1.7848117503333332

> <ALOGPS_LOGS>
-3.16

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-2.830371964296339

> <JCHEM_POLAR_SURFACE_AREA>
48.67

> <JCHEM_REFRACTIVITY>
56.85290000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.48e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
bergapten

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 20-MAY-19   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: Bergapten                                         
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   20-MAY-19         0                                  
HETATM    1  C   UNK     0       4.924   0.237   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       6.258  -0.533   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       6.258  -2.073   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       7.591  -2.843   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       8.925  -2.073   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      10.259  -2.843   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      10.259  -4.383   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      11.592  -5.153   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       8.925  -5.153   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       7.591  -4.383   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       6.258  -5.153   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.924  -4.383   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       4.924  -2.843   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       3.459  -2.367   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       2.554  -3.613   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       3.459  -4.859   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   13                                                  
CONECT    4    3    5   10                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10                                                       
CONECT   10    9    4   11                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13   16                                                  
CONECT   13   12    3   14                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   12                                                       
MASTER        0    0    0    0    0    0    0    0   16    0   36    0
END

View in JSmol

Synonyms

Value	Source
4-Methoxy-7H-furo[3,2-g][1]benzopyran-7-one	ChEBI
5-Methoxyfuranocoumarin	ChEBI
5-Methoxypsoralene	ChEBI
Bergaptene	ChEBI
Heraclin	ChEBI
Majudin	ChEBI
O-Methylbergaptol	ChEBI
5-Methoxypsoralen	Kegg
Pentaderm	Kegg
4-Methoxy-7H-furo(3,2-g)(1)benzopyran-7-one	HMDB
4-Methoxy-7H-furo[3,2-g]benzopyran-7-one	HMDB
4-Methoxy-7H-furo[3,2-g]chromen-7-one	HMDB
4-Methoxy-furo[3,2-g]chromen-7-one	HMDB
4-Methoxyfuro[3,2-g]benzopyrane-7-one	HMDB
5-Methoxy psoralen	HMDB
5-Methoxy-6,7-furanocoumarin	HMDB
5-Methoxypsoralen (obsol.)	HMDB
5-MOP	HMDB
6-Hydroxy-4-methoxy-5-benzofuranacrylic acid, gamma-lactone	HMDB
Bergaptan	HMDB
Psoraderm	HMDB
Bergapten	ChEBI
5 Methoxypsoralen	MeSH
5 Methoxy psoralen	MeSH

Chemical Formula

C₁₂H₈O₄

Average Mass

216.1920 Da

Monoisotopic Mass

216.04226 Da

IUPAC Name

4-methoxy-7H-furo[3,2-g]chromen-7-one

Traditional Name

bergapten

CAS Registry Number

Not Available

SMILES

COC1=C2C=CC(=O)OC2=CC2=C1C=CO2

InChI Identifier

InChI=1S/C12H8O4/c1-14-12-7-2-3-11(13)16-10(7)6-9-8(12)4-5-15-9/h2-6H,1H3

InChI Key

BGEBZHIAGXMEMV-UHFFFAOYSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
HMBC NMR	[¹H, ¹³C] NMR Spectrum (2D, 500 MHz, CDCl3, experimental)	mate.erdelyi@kemi.uu.se	Not Available	Not Available	2023-04-15	View Spectrum
HSQC NMR	[¹H, ¹³C] NMR Spectrum (2D, 500 MHz, CDCl3, experimental)	mate.erdelyi@kemi.uu.se	Not Available	Not Available	2023-04-15	View Spectrum
TOCSY NMR	[¹H, ¹H] NMR Spectrum (2D, 500 MHz, CDCl3, experimental)	mate.erdelyi@kemi.uu.se	Not Available	Not Available	2023-04-15	View Spectrum
NOESY NMR	[¹H, ¹H] NMR Spectrum (2D, 500 MHz, CDCl3, experimental)	mate.erdelyi@kemi.uu.se	Not Available	Not Available	2023-04-15	View Spectrum
COSY NMR	[¹H, ¹H] NMR Spectrum (2D, 500 MHz, CDCl3, experimental)	mate.erdelyi@kemi.uu.se	Not Available	Not Available	2023-04-15	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, CDCl3, experimental)	mate.erdelyi@kemi.uu.se	Not Available	Not Available	2023-04-15	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, CDCl3, experimental)	mate.erdelyi@kemi.uu.se	Not Available	Not Available	2023-04-15	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, CDCl₃, experimental)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View

Chemical Shift Submissions

Not Available

Species

Species of Origin

Not Available

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 5-methoxypsoralens. These are psoralens containing a methoxy group attached at the C5 position of the psoralen group.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Coumarins and derivatives

Sub Class

Furanocoumarins

Direct Parent

5-methoxypsoralens

Alternative Parents

Substituents

5-methoxypsoralen
Benzopyran
1-benzopyran
Benzofuran
Anisole
Alkyl aryl ether
Pyranone
Pyran
Benzenoid
Furan
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

organic heterotricyclic compound (CHEBI:18293 )
psoralens (CHEBI:18293 )
5-methoxyfurocoumarin (CHEBI:18293 )
Furanocoumarins (C01557 )
a coumarin (5-METHOXYFURANOCOUMARIN )

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	2.12	ALOGPS
logP	1.78	ChemAxon
logS	-3.2	ALOGPS
pKa (Strongest Basic)	-2.8	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	48.67 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	56.85 m³·mol⁻¹	ChemAxon
Polarizability	20.87 Å³	ChemAxon
Number of Rings	3	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

HMDB0030637

DrugBank ID

DB12216

Phenol Explorer Compound ID

FoodDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

5-METHOXYFURANOCOUMARIN

BiGG ID

Not Available

Wikipedia Link

Bergapten

METLIN ID

Not Available

PubChem Compound

2355

PDB ID

Not Available

ChEBI ID

18293

Good Scents ID

Not Available

References

General References

Luszczki JJ, Andres-Mach M, Glensk M, Skalicka-Wozniak K: Anticonvulsant effects of four linear furanocoumarins, bergapten, imperatorin, oxypeucedanin, and xanthotoxin, in the mouse maximal electroshock-induced seizure model: a comparative study. Pharmacol Rep. 2010 Nov-Dec;62(6):1231-6. [PubMed:21273683 ]
Tsassi VB, Hussain H, Meffo BY, Kouam SF, Dongo E, Schulz B, Greene IR, Krohn K: Antimicrobial coumarins from the stem bark of Afraegle paniculata. Nat Prod Commun. 2010 Apr;5(4):559-61. [PubMed:20433072 ]
Liu WX, Jia FL, He YY, Zhang BX: Protective effects of 5-methoxypsoralen against acetaminophen-induced hepatotoxicity in mice. World J Gastroenterol. 2012 May 14;18(18):2197-202. doi: 10.3748/wjg.v18.i18.2197. [PubMed:22611312 ]

Showing NP-Card for Bergapin (NP0331583)

MOL for NP0331583 (Bergapin)

3D MOL for NP0331583 (Bergapin)

3D SDF for NP0331583 (Bergapin)

3D-SDF for NP0331583 (Bergapin)

PDB for NP0331583 (Bergapin)

3D PDB for NP0331583 (Bergapin)

SMILES for NP0331583 (Bergapin)

INCHI for NP0331583 (Bergapin)

Structure for NP0331583 (Bergapin)

3D Structure for NP0331583 (Bergapin)