NP-MRD: Showing NP-Card for Protopseudohypericin (NP0073936)

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Record Information

Version

2.0

Created at

2022-04-28 19:08:45 UTC

Updated at

2022-04-28 19:08:45 UTC

NP-MRD ID

NP0073936

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Protopseudohypericin

Description

7,11,13,16,18,22-Hexahydroxy-5-(hydroxymethyl)-24-methylheptacyclo[13.11.1.1²,¹⁰.0³,⁸.0¹⁹,²⁷.0²¹,²⁶.0¹⁴,²⁸]Octacosa-1(27),2(28),3(8),4,6,10,12,14,16,18,21(26),22,24-tridecaene-9,20-dione belongs to the class of organic compounds known as perylenequinones. These are heterocyclic compounds characterized by two 8-hydroxy-1,4-dihydronaphthalen-1-one moieties joined together one or two CC-bonds. Protopseudohypericin is found in Hypericum hirsutum, Hypericum perforatum and Hypericum pulchrum. 7,11,13,16,18,22-Hexahydroxy-5-(hydroxymethyl)-24-methylheptacyclo[13.11.1.1²,¹⁰.0³,⁸.0¹⁹,²⁷.0²¹,²⁶.0¹⁴,²⁸]Octacosa-1(27),2(28),3(8),4,6,10,12,14,16,18,21(26),22,24-tridecaene-9,20-dione is a strong basic compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652310091720322D          

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M  END

     RDKit          3D

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M  END


  Mrv1652310091720322D          

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M  END
> <DATABASE_ID>
NP0073936

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC1=CC2=C(C(O)=C1)C(=O)C1=C(O)C=C(O)C3=C4C(O)=CC(O)=C5C(=O)C6=C(C=C(CO)C=C6O)C(C2=C13)=C45

> <INCHI_IDENTIFIER>
InChI=1S/C30H18O9/c1-9-2-11-19(13(32)3-9)29(38)25-17(36)6-15(34)23-24-16(35)7-18(37)26-28(24)22(21(11)27(23)25)12-4-10(8-31)5-14(33)20(12)30(26)39/h2-7,31-37H,8H2,1H3

> <INCHI_KEY>
QFAPJWSQKUFHAP-UHFFFAOYSA-N

> <FORMULA>
C30H18O9

> <MOLECULAR_WEIGHT>
522.465

> <EXACT_MASS>
522.09508216

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
57

> <JCHEM_AVERAGE_POLARIZABILITY>
52.14180992088374

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
7

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
7,11,13,16,18,22-hexahydroxy-5-(hydroxymethyl)-24-methylheptacyclo[13.11.1.1^{2,10}.0^{3,8}.0^{19,27}.0^{21,26}.0^{14,28}]octacosa-1(27),2(28),3(8),4,6,10,12,14,16,18,21(26),22,24-tridecaene-9,20-dione

> <ALOGPS_LOGP>
3.33

> <JCHEM_LOGP>
6.7435441879999996

> <ALOGPS_LOGS>
-4.76

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
7

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.811607813367603

> <JCHEM_PKA_STRONGEST_ACIDIC>
6.343886290224228

> <JCHEM_PKA_STRONGEST_BASIC>
3.6630501526052885

> <JCHEM_POLAR_SURFACE_AREA>
175.75

> <JCHEM_REFRACTIVITY>
142.00830000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
9.03e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
7,11,13,16,18,22-hexahydroxy-5-(hydroxymethyl)-24-methylheptacyclo[13.11.1.1^{2,10}.0^{3,8}.0^{19,27}.0^{21,26}.0^{14,28}]octacosa-1(27),2(28),3(8),4,6,10,12,14,16,18,21(26),22,24-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      12.066   3.680   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      10.050   1.934   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      12.570   1.061   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       9.042   3.098   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       8.538   5.718   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.521  -4.178   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.489   0.479   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      11.058   4.844   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      11.562   2.225   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       9.546   4.553   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       9.546   0.479   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       7.530   2.807   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      12.066  -0.394   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       7.026   5.427   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       5.513  -3.013   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       3.497  -0.685   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       8.034  -3.887   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       2.993   1.934   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      10.554  -0.685   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       6.521   3.971   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       8.034   0.188   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       7.026   1.352   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       6.017  -1.558   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       5.009  -0.394   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       8.538  -2.431   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       4.505   2.225   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       7.530  -1.267   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       5.513   1.061   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      10.050  -2.140   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       5.009   3.680   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0      11.562   6.300   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0      13.075  -1.558   0.000  0.00  0.00           O+0
HETATM   33  O   UNK     0       6.017   6.591   0.000  0.00  0.00           O+0
HETATM   34  O   UNK     0       4.001  -3.304   0.000  0.00  0.00           O+0
HETATM   35  O   UNK     0       2.993  -2.140   0.000  0.00  0.00           O+0
HETATM   36  O   UNK     0       9.042  -5.051   0.000  0.00  0.00           O+0
HETATM   37  O   UNK     0       1.985   3.098   0.000  0.00  0.00           O+0
HETATM   38  O   UNK     0      11.058  -3.304   0.000  0.00  0.00           O+0
HETATM   39  O   UNK     0       4.001   4.844   0.000  0.00  0.00           O+0
CONECT    1    9                                                            
CONECT    2    9   11                                                       
CONECT    3    9   13                                                       
CONECT    4   10   12                                                       
CONECT    5   10   14                                                       
CONECT    6   15   17                                                       
CONECT    7   16   18                                                       
CONECT    8   10   31                                                       
CONECT    9    1    2    3                                                  
CONECT   10    4    5    8                                                  
CONECT   11    2   19   21                                                  
CONECT   12    4   20   22                                                  
CONECT   13    3   19   32                                                  
CONECT   14    5   20   33                                                  
CONECT   15    6   23   34                                                  
CONECT   16    7   24   35                                                  
CONECT   17    6   25   36                                                  
CONECT   18    7   26   37                                                  
CONECT   19   11   13   29                                                  
CONECT   20   12   14   30                                                  
CONECT   21   11   22   27                                                  
CONECT   22   12   21   28                                                  
CONECT   23   15   24   27                                                  
CONECT   24   16   23   28                                                  
CONECT   25   17   27   29                                                  
CONECT   26   18   28   30                                                  
CONECT   27   21   23   25                                                  
CONECT   28   22   24   26                                                  
CONECT   29   19   25   38                                                  
CONECT   30   20   26   39                                                  
CONECT   31    8                                                            
CONECT   32   13                                                            
CONECT   33   14                                                            
CONECT   34   15                                                            
CONECT   35   16                                                            
CONECT   36   17                                                            
CONECT   37   18                                                            
CONECT   38   29                                                            
CONECT   39   30                                                            
MASTER        0    0    0    0    0    0    0    0   39    0   90    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₃₀H₁₈O₉

Average Mass

522.4650 Da

Monoisotopic Mass

522.09508 Da

IUPAC Name

7,11,13,16,18,22-hexahydroxy-5-(hydroxymethyl)-24-methylheptacyclo[13.11.1.1^{2,10}.0^{3,8}.0^{19,27}.0^{21,26}.0^{14,28}]octacosa-1(27),2(28),3(8),4,6,10,12,14,16,18,21(26),22,24-tridecaene-9,20-dione

Traditional Name

CAS Registry Number

Not Available

SMILES

CC1=CC2=C(C(O)=C1)C(=O)C1=C(O)C=C(O)C3=C4C(O)=CC(O)=C5C(=O)C6=C(C=C(CO)C=C6O)C(C2=C13)=C45

InChI Identifier

InChI=1S/C30H18O9/c1-9-2-11-19(13(32)3-9)29(38)25-17(36)6-15(34)23-24-16(35)7-18(37)26-28(24)22(21(11)27(23)25)12-4-10(8-31)5-14(33)20(12)30(26)39/h2-7,31-37H,8H2,1H3

InChI Key

QFAPJWSQKUFHAP-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 hirsutum	LOTUS Database	35616633
Hypericum perforatum	Plant	KNApSAcK
Hypericum pulchrum	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as perylenequinones. These are heterocyclic compounds characterized by two 8-hydroxy-1,4-dihydronaphthalen-1-one moieties joined together one or two CC-bonds.

Kingdom

Organic compounds

Super Class

Benzenoids

Class

Perylenequinones

Sub Class

Not Available

Direct Parent

Perylenequinones

Alternative Parents

Substituents

Perylenequinone
Phenanthrol
Anthracene
Phenanthrene
2-naphthol
1-naphthol
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Phenol
Vinylogous acid
Polyol
Hydrocarbon derivative
Organic oxide
Organooxygen compound
Organic oxygen compound
Alcohol
Primary alcohol
Aromatic alcohol
Aromatic homopolycyclic compound

Molecular Framework

Aromatic homopolycyclic 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	3.33	ALOGPS
logP	6.74	ChemAxon
logS	-4.8	ALOGPS
pKa (Strongest Acidic)	6.34	ChemAxon
pKa (Strongest Basic)	3.66	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	142.01 m³·mol⁻¹	ChemAxon
Polarizability	52.14 Å³	ChemAxon
Number of Rings	7	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

HMDB0171458

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

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

5490324

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Protopseudohypericin (NP0073936)

MOL for NP0073936 (Protopseudohypericin)

3D MOL for NP0073936 (Protopseudohypericin)

3D SDF for NP0073936 (Protopseudohypericin)

3D-SDF for NP0073936 (Protopseudohypericin)

PDB for NP0073936 (Protopseudohypericin)

3D PDB for NP0073936 (Protopseudohypericin)

SMILES for NP0073936 (Protopseudohypericin)

INCHI for NP0073936 (Protopseudohypericin)

Structure for NP0073936 (Protopseudohypericin)

3D Structure for NP0073936 (Protopseudohypericin)