NP-MRD: Showing NP-Card for Hypericin (NP0051614)

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Record Information

Version

2.0

Created at

2022-04-27 22:54:51 UTC

Updated at

2022-04-27 22:54:52 UTC

NP-MRD ID

NP0051614

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Hypericin

Description

Hypericin, also known as hipericina or hypericum red, belongs to the class of organic compounds known as benzopyrenes. These are organic compounds containing a benzene fused to a pyrene(benzo[def]phenanthrene) ring system. Thus, hypericin is considered to be an aromatic polyketide lipid molecule. These reactions are photosensitive and take place under exposure to light and using the enzyme Hyp-1. Hypericin is believed to act as an antibiotic, antiviral and non-specific kinase inhibitor. Hypericin is a naphthodianthrone, an anthraquinone derivative which, together with hyperforin, is one of the principal active constituents of Hypericum (Saint John's wort). Hypericin is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral. Outside of the human body, Hypericin has been detected, but not quantified in, a few different foods, such as alcoholic beverages, herbs and spices, and tea. This could make hypericin a potential biomarker for the consumption of these foods. The large chromophore system in the molecule means that it can cause photosensitivity when ingested beyond threshold amounts. Hypericin derives from polyketides cyclisation. Photosensitivity is often seen in animals that have been allowed to graze on St. John's Wort. Hypericin is found in Canariomyces subthermophilus, Cortinarius austrovenetus, Fagopyrum esculentum, Hypericum barbatum Jacq. , Hypericum bithynicum, Hypericum elodes, Hypericum erectum, Hypericum faberi, Hypericum grandifolium, Hypericum hirsutum, Hypericum hirsutum L., Hypericum linarioides BOSSE, Hypericum maculatum, Hypericum maculatum Crantz , Hypericum perforatum , Hypericum rumeliacum, Hypericum rumeliacum BOISS., Hypericum sampsonii, Hypericum spp., Hypericum tetrapterum, Hypericum tetrapterum Fries , Hypericum triquetrifolium, Hypericum venustum, Hypericum wightianum and Thielavia subthermophila. Hypericin was first documented in 1998 (PMID: 9796444). Isolated hypericin does not display this activity, but does have some affinity for NMDA receptors (PMID: 11458458) (PMID: 12770617).

Structure

MOL 3D MOL SDF PDB SMILES InChI

  Mrv0541 05061307412D          

 38 45  0  0  0  0            999 V2000
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M  END

     RDKit          3D

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M  END

  Mrv0541 05061307412D          

 38 45  0  0  0  0            999 V2000
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M  END
> <DATABASE_ID>
NP0051614

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC1=CC(O)=C2C(=O)C3=C(O)C=C(O)C4=C3C3=C2C1=C1C(C)=CC(O)=C2C(=O)C5=C(O)C=C(O)C4=C5C3=C12

> <INCHI_IDENTIFIER>
InChI=1S/C30H16O8/c1-7-3-9(31)19-23-15(7)16-8(2)4-10(32)20-24(16)28-26-18(12(34)6-14(36)22(26)30(20)38)17-11(33)5-13(35)21(29(19)37)25(17)27(23)28/h3-6,31-36H,1-2H3

> <INCHI_KEY>
BTXNYTINYBABQR-UHFFFAOYSA-N

> <FORMULA>
C30H16O8

> <MOLECULAR_WEIGHT>
504.4432

> <EXACT_MASS>
504.084517488

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_AVERAGE_POLARIZABILITY>
50.95649342842092

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
5,7,11,18,22,24-hexahydroxy-13,16-dimethyloctacyclo[13.11.1.1²,¹⁰.0³,⁸.0⁴,²⁵.0¹⁹,²⁷.0²¹,²⁶.0¹⁴,²⁸]octacosa-1(27),2(28),3,5,7,10,12,14,16,18,21,23,25-tridecaene-9,20-dione

> <ALOGPS_LOGP>
3.92

> <JCHEM_LOGP>
7.698294890666666

> <ALOGPS_LOGS>
-4.84

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
8

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-4

> <JCHEM_PKA>
2.1179088207448276

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.3879350822145318

> <JCHEM_PKA_STRONGEST_BASIC>
16.114078792380027

> <JCHEM_POLAR_SURFACE_AREA>
155.52

> <JCHEM_REFRACTIVITY>
139.3118

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
7.32e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
hypericin

> <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       0.326   8.300   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.334   9.464   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.179   5.681   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.854  10.338   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       5.870   0.442   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       9.903   5.099   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.830   6.845   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.846   9.173   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.326   4.226   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       5.366  10.047   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       6.879   1.607   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       8.895   3.935   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       4.358   0.733   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       9.399   6.554   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       2.342   6.554   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       3.350   7.718   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       6.374   3.062   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       7.383   4.226   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       1.838   3.935   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       5.870   8.591   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       3.854   2.189   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       7.887   6.845   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       2.846   5.099   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       4.862   7.427   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       4.862   3.353   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       6.879   5.681   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       4.358   4.808   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       5.366   5.972   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       2.342   2.480   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       7.383   8.300   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0      -0.683   3.062   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0       6.374  11.211   0.000  0.00  0.00           O+0
HETATM   33  O   UNK     0       8.391   1.316   0.000  0.00  0.00           O+0
HETATM   34  O   UNK     0       9.399   2.480   0.000  0.00  0.00           O+0
HETATM   35  O   UNK     0       3.350  -0.431   0.000  0.00  0.00           O+0
HETATM   36  O   UNK     0      10.407   7.718   0.000  0.00  0.00           O+0
HETATM   37  O   UNK     0       1.334   1.316   0.000  0.00  0.00           O+0
HETATM   38  O   UNK     0       8.391   9.464   0.000  0.00  0.00           O+0
CONECT    1    7                                                            
CONECT    2    8                                                            
CONECT    3    7    9                                                       
CONECT    4    8   10                                                       
CONECT    5   11   13                                                       
CONECT    6   12   14                                                       
CONECT    7    1    3   15                                                  
CONECT    8    2    4   16                                                  
CONECT    9    3   19   31                                                  
CONECT   10    4   20   32                                                  
CONECT   11    5   17   33                                                  
CONECT   12    6   18   34                                                  
CONECT   13    5   21   35                                                  
CONECT   14    6   22   36                                                  
CONECT   15    7   16   23                                                  
CONECT   16    8   15   24                                                  
CONECT   17   11   18   25                                                  
CONECT   18   12   17   26                                                  
CONECT   19    9   23   29                                                  
CONECT   20   10   24   30                                                  
CONECT   21   13   25   29                                                  
CONECT   22   14   26   30                                                  
CONECT   23   15   19   27                                                  
CONECT   24   16   20   28                                                  
CONECT   25   17   21   27                                                  
CONECT   26   18   22   28                                                  
CONECT   27   23   25   28                                                  
CONECT   28   24   26   27                                                  
CONECT   29   19   21   37                                                  
CONECT   30   20   22   38                                                  
CONECT   31    9                                                            
CONECT   32   10                                                            
CONECT   33   11                                                            
CONECT   34   12                                                            
CONECT   35   13                                                            
CONECT   36   14                                                            
CONECT   37   29                                                            
CONECT   38   30                                                            
MASTER        0    0    0    0    0    0    0    0   38    0   90    0
END

View in JSmol

Synonyms

Value	Source
1:6:8:10:11:13-Hexahydroxy-3:4-dimethyl-meso-naphthodianthrene-7:14-dione	ChEBI
Hipericina	ChEBI
Hypericine	ChEBI
Hypericum red	ChEBI
Hyperizin	ChEBI
1,3,4,6,8,13-Hexahydroxy-10,11-dimethylphenanthro[1,10,9,8-opqra]perylene-7,14-dione, 9ci	HMDB
4,5,7,4',5',7'-Hexahydroxy-2,2'-dimethylnaphthodianthrone	HMDB
Hypericin & visible light	HMDB
Hypericin from hypericum perforatum	HMDB
Hypericum extract	HMDB
Mycoporphyrin	HMDB
Vimrxyn	HMDB
mono-(123I)iodohypericin	MeSH

Chemical Formula

C₃₀H₁₆O₈

Average Mass

504.4432 Da

Monoisotopic Mass

504.08452 Da

IUPAC Name

5,7,11,18,22,24-hexahydroxy-13,16-dimethyloctacyclo[13.11.1.1²,¹⁰.0³,⁸.0⁴,²⁵.0¹⁹,²⁷.0²¹,²⁶.0¹⁴,²⁸]octacosa-1(27),2(28),3,5,7,10,12,14,16,18,21,23,25-tridecaene-9,20-dione

Traditional Name

hypericin

CAS Registry Number

Not Available

SMILES

CC1=CC(O)=C2C(=O)C3=C(O)C=C(O)C4=C3C3=C2C1=C1C(C)=CC(O)=C2C(=O)C5=C(O)C=C(O)C4=C5C3=C12

InChI Identifier

InChI=1S/C30H16O8/c1-7-3-9(31)19-23-15(7)16-8(2)4-10(32)20-24(16)28-26-18(12(34)6-14(36)22(26)30(20)38)17-11(33)5-13(35)21(29(19)37)25(17)27(23)28/h3-6,31-36H,1-2H3

InChI Key

BTXNYTINYBABQR-UHFFFAOYSA-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
Canariomyces subthermophilus	LOTUS Database	35616633
Cortinarius austrovenetus	LOTUS Database	35616633
Fagopyrum esculentum	LOTUS Database	35616633
Hypericum barbatum Jacq.	Plant	KNApSAcK
Hypericum bithynicum	LOTUS Database	35616633
Hypericum elodes	LOTUS Database	35616633
Hypericum erectum	Plant	KNApSAcK
Hypericum faberi	Plant	KNApSAcK
Hypericum grandifolium	LOTUS Database	35616633
Hypericum hirsutum	LOTUS Database	35616633
Hypericum hirsutum L.	Plant	KNApSAcK
Hypericum linarioides BOSSE	Plant	KNApSAcK
Hypericum maculatum	LOTUS Database	35616633
Hypericum maculatum Crantz	Plant	KNApSAcK
Hypericum perforatum	Plant	KNApSAcK
Hypericum rumeliacum	LOTUS Database	35616633
Hypericum rumeliacum BOISS.	Plant	KNApSAcK
Hypericum sampsonii	Plant	KNApSAcK
Hypericum spp.	Plant	KNApSAcK
Hypericum tetrapterum	LOTUS Database	35616633
Hypericum tetrapterum Fries	Plant	KNApSAcK
Hypericum triquetrifolium	LOTUS Database	35616633
Hypericum venustum	LOTUS Database	35616633
Hypericum wightianum	Plant	KNApSAcK
Thielavia subthermophila	Fungi	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as benzopyrenes. These are organic compounds containing a benzene fused to a pyrene(benzo[def]phenanthrene) ring system.

Kingdom

Super Class

Class

Sub Class

Direct Parent

Alternative Parents

Substituents

Benzo-a-pyrene
Benzo-e-pyrene
Phenanthro-perylenequinone
Perylenequinone
Chrysene
Triphenylene
Phenanthrol
Phenanthrene
Anthracene
1-naphthol
2-naphthol
1-hydroxy-2-unsubstituted benzenoid
Vinylogous acid
Polyol
Organic oxide
Organooxygen compound
Organic oxygen compound
Hydrocarbon derivative
Aromatic homopolycyclic compound

Molecular Framework

Aromatic homopolycyclic compounds

External Descriptors

carbopolycyclic compound (CHEBI:5835 )
Anthracenes and phenanthrenes (C07606 )
Anthrone type (C07606 )
Anthracenes and phenanthrenes (LMPK13040001 )

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	3.92	ALOGPS
logP	7.7	ChemAxon
logS	-4.8	ALOGPS
pKa (Strongest Acidic)	1.39	ChemAxon
pKa (Strongest Basic)	16.11	ChemAxon
Physiological Charge	-4	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	155.52 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	139.31 m³·mol⁻¹	ChemAxon
Polarizability	50.96 Å³	ChemAxon
Number of Rings	8	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

HMDB0034271

DrugBank ID

DB13014

Phenol Explorer Compound ID

Not Available

FoodDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Hypericin

METLIN ID

Not Available

PubChem Compound

5281051

PDB ID

Not Available

ChEBI ID

5835

Good Scents ID

Not Available

References

General References

Kang BY, Chung SW, Kim TS: Inhibition of interleukin-12 production in lipopolysaccharide-activated mouse macrophages by hpyericin, an active component of Hypericum perforatum. Planta Med. 2001 Jun;67(4):364-6. doi: 10.1055/s-2001-14333. [PubMed:11458458 ]
Butterweck V, Christoffel V, Nahrstedt A, Petereit F, Spengler B, Winterhoff H: Step by step removal of hyperforin and hypericin: activity profile of different Hypericum preparations in behavioral models. Life Sci. 2003 Jun 20;73(5):627-39. doi: 10.1016/s0024-3205(03)00314-x. [PubMed:12770617 ]
Park J, English DS, Wannemuehler Y, Carpenter S, Petrich JW: The role of oxygen in the antiviral activity of hypericin and hypocrellin. Photochem Photobiol. 1998 Oct;68(4):593-7. [PubMed:9796444 ]

Showing NP-Card for Hypericin (NP0051614)

MOL for NP0051614 (Hypericin)

3D MOL for NP0051614 (Hypericin)

3D SDF for NP0051614 (Hypericin)

3D-SDF for NP0051614 (Hypericin)

PDB for NP0051614 (Hypericin)

3D PDB for NP0051614 (Hypericin)

SMILES for NP0051614 (Hypericin)

INCHI for NP0051614 (Hypericin)

Structure for NP0051614 (Hypericin)

3D Structure for NP0051614 (Hypericin)