NP-MRD: Showing NP-Card for Pseudohypericin (NP0051633)

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Record Information

Version

2.0

Created at

2022-04-27 22:55:47 UTC

Updated at

2022-04-27 22:55:48 UTC

NP-MRD ID

NP0051633

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Pseudohypericin

Description

Pseudohypericin 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, pseudohypericin is considered to be an aromatic polyketide lipid molecule. Pseudohypericin is an aromatic polycyclic dione that is very closely related to hypericin. Pseudohypericin is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral. It may also contribute to the potential antidepressant effect of Hypericum perforatum extracts. It is found most commonly in the St. John's wort family of plants, namely in Hypericum perforatum. Pseudohypericin is found in Hypericum barbatum Jacq. , Hypericum elodes, Hypericum humifusum, Hypericum maculatum, Hypericum maculatum Crantz , Hypericum perforatum , Hypericum rumeliacum BOISS., Hypericum tetrapterum Fries and Hypericum triquetrifolium . In preliminary studies in animal models, pseudohypericin has shown antiviral effects.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652310091723132D          

 39 46  0  0  0  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652310091723132D          

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M  END
> <DATABASE_ID>
NP0051633

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C30H16O9/c1-7-2-9(32)19-23-15(7)16-8(6-31)3-10(33)20-24(16)28-26-18(12(35)5-14(37)22(26)30(20)39)17-11(34)4-13(36)21(29(19)38)25(17)27(23)28/h2-5,31-37H,6H2,1H3

> <INCHI_KEY>
YXBUQQDFTYOHQI-UHFFFAOYSA-N

> <FORMULA>
C30H16O9

> <MOLECULAR_WEIGHT>
520.449

> <EXACT_MASS>
520.079432095

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
55

> <JCHEM_AVERAGE_POLARIZABILITY>
51.881324426594446

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
7

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
5,7,11,18,22,24-hexahydroxy-13-(hydroxymethyl)-16-methyloctacyclo[13.11.1.1^{2,10}.0^{3,8}.0^{4,25}.0^{19,27}.0^{21,26}.0^{14,28}]octacosa-1(27),2(28),3,5,7,10,12,14,16,18,21,23,25-tridecaene-9,20-dione

> <ALOGPS_LOGP>
3.19

> <JCHEM_LOGP>
6.4175237339999995

> <ALOGPS_LOGS>
-4.54

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
8

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.988107520077991

> <JCHEM_PKA_STRONGEST_ACIDIC>
6.033786833021436

> <JCHEM_PKA_STRONGEST_BASIC>
3.3335644449307855

> <JCHEM_POLAR_SURFACE_AREA>
175.75

> <JCHEM_REFRACTIVITY>
141.0865

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.52e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5,7,11,18,22,24-hexahydroxy-13-(hydroxymethyl)-16-methyloctacyclo[13.11.1.1^{2,10}.0^{3,8}.0^{4,25}.0^{19,27}.0^{21,26}.0^{14,28}]octacosa-1(27),2(28),3,5,7,10,12,14,16,18,21,23,25-tridecaene-9,20-dione

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 09-OCT-17   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   09-OCT-17         0                                  
HETATM    1  C   UNK     0       0.326   8.300   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.179   5.681   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       3.854  10.338   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.870   0.442   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       9.903   5.099   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.334   9.464   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       6.375   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       0.830  10.920   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0      -0.683   3.062   0.000  0.00  0.00           O+0
HETATM   33  O   UNK     0       6.375  11.211   0.000  0.00  0.00           O+0
HETATM   34  O   UNK     0       8.391   1.316   0.000  0.00  0.00           O+0
HETATM   35  O   UNK     0       9.399   2.480   0.000  0.00  0.00           O+0
HETATM   36  O   UNK     0       3.350  -0.431   0.000  0.00  0.00           O+0
HETATM   37  O   UNK     0      10.407   7.718   0.000  0.00  0.00           O+0
HETATM   38  O   UNK     0       1.334   1.316   0.000  0.00  0.00           O+0
HETATM   39  O   UNK     0       8.391   9.464   0.000  0.00  0.00           O+0
CONECT    1    7                                                            
CONECT    2    7    9                                                       
CONECT    3    8   10                                                       
CONECT    4   11   13                                                       
CONECT    5   12   14                                                       
CONECT    6    8   31                                                       
CONECT    7    1    2   15                                                  
CONECT    8    3    6   16                                                  
CONECT    9    2   19   32                                                  
CONECT   10    3   20   33                                                  
CONECT   11    4   17   34                                                  
CONECT   12    5   18   35                                                  
CONECT   13    4   21   36                                                  
CONECT   14    5   22   37                                                  
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   38                                                  
CONECT   30   20   22   39                                                  
CONECT   31    6                                                            
CONECT   32    9                                                            
CONECT   33   10                                                            
CONECT   34   11                                                            
CONECT   35   12                                                            
CONECT   36   13                                                            
CONECT   37   14                                                            
CONECT   38   29                                                            
CONECT   39   30                                                            
MASTER        0    0    0    0    0    0    0    0   39    0   92    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₃₀H₁₆O₉

Average Mass

520.4490 Da

Monoisotopic Mass

520.07943 Da

IUPAC Name

5,7,11,18,22,24-hexahydroxy-13-(hydroxymethyl)-16-methyloctacyclo[13.11.1.1^{2,10}.0^{3,8}.0^{4,25}.0^{19,27}.0^{21,26}.0^{14,28}]octacosa-1(27),2(28),3,5,7,10,12,14,16,18,21,23,25-tridecaene-9,20-dione

Traditional Name

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C30H16O9/c1-7-2-9(32)19-23-15(7)16-8(6-31)3-10(33)20-24(16)28-26-18(12(35)5-14(37)22(26)30(20)39)17-11(34)4-13(36)21(29(19)38)25(17)27(23)28/h2-5,31-37H,6H2,1H3

InChI Key

YXBUQQDFTYOHQI-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
Hypericum barbatum Jacq.	Plant	KNApSAcK
Hypericum elodes	LOTUS Database	35616633
Hypericum humifusum	LOTUS Database	35616633
Hypericum maculatum	LOTUS Database	35616633
Hypericum maculatum Crantz	Plant	KNApSAcK
Hypericum perforatum	Plant	KNApSAcK
Hypericum rumeliacum BOISS.	Plant	KNApSAcK
Hypericum tetrapterum Fries	Plant	KNApSAcK
Hypericum triquetrifolium	Plant	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
Anthracene
Phenanthrene
1-naphthol
2-naphthol
1-hydroxy-2-unsubstituted benzenoid
Vinylogous acid
Polyol
Aromatic alcohol
Primary alcohol
Organic oxide
Organooxygen compound
Alcohol
Organic oxygen compound
Hydrocarbon derivative
Aromatic homopolycyclic compound

Molecular Framework

Aromatic homopolycyclic compounds

External Descriptors

ortho- and peri-fused polycyclic arene (CHEBI:8605 )
Anthracenes and phenanthrenes (C10392 )
Anthracenes and phenanthrenes (LMPK13040014 )

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	3.19	ALOGPS
logP	6.42	ChemAxon
logS	-4.5	ALOGPS
pKa (Strongest Acidic)	6.03	ChemAxon
pKa (Strongest Basic)	3.33	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	7	ChemAxon
Polar Surface Area	175.75 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	141.09 m³·mol⁻¹	ChemAxon
Polarizability	51.88 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

HMDB0172346

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00002855

Chemspider ID

Not Available

KEGG Compound ID

C10392

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Pseudohypericin

METLIN ID

Not Available

PubChem Compound

5281751

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Pseudohypericin (NP0051633)

MOL for NP0051633 (Pseudohypericin)

3D MOL for NP0051633 (Pseudohypericin)

3D SDF for NP0051633 (Pseudohypericin)

3D-SDF for NP0051633 (Pseudohypericin)

PDB for NP0051633 (Pseudohypericin)

3D PDB for NP0051633 (Pseudohypericin)

SMILES for NP0051633 (Pseudohypericin)

INCHI for NP0051633 (Pseudohypericin)

Structure for NP0051633 (Pseudohypericin)

3D Structure for NP0051633 (Pseudohypericin)