NP-MRD: Showing NP-Card for Hypercalin B (NP0051726)

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Record Information

Version

2.0

Created at

2022-04-27 22:59:02 UTC

Updated at

2022-04-27 22:59:02 UTC

NP-MRD ID

NP0051726

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Hypercalin B

Description

2-Benzoyl-3,5-dihydroxy-4-{[(1R,2S,5S)-2-hydroxy-2-methyl-5-(prop-1-en-2-yl)cyclopentyl]methyl}-6,6-bis(3-methylbut-2-en-1-yl)cyclohexa-2,4-dien-1-one belongs to the class of organic compounds known as aromatic monoterpenoids. These are monoterpenoids containing at least one aromatic ring. Hypercalin B is found in Hypericum ascyron , Hypericum beanii, Hypericum calycinum and Hypericum calycunum. Based on a literature review very few articles have been published on 2-benzoyl-3,5-dihydroxy-4-{[(1R,2S,5S)-2-hydroxy-2-methyl-5-(prop-1-en-2-yl)cyclopentyl]methyl}-6,6-bis(3-methylbut-2-en-1-yl)cyclohexa-2,4-dien-1-one.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282200592D          

 38 40  0  0  1  0            999 V2000
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 29 37  1  6  0  0  0
 10 38  1  0  0  0  0
M  END

     RDKit          3D

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M  END


  Mrv1652304282200592D          

 38 40  0  0  1  0            999 V2000
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   -2.4492   -0.0937    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6242   -0.0937    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.3191   -0.9811    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3258   -1.8993    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3071   -1.0237    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6330    1.8220    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6672    1.9722    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8342   -0.7942    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  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
  1  6  1  0  0  0  0
  5  7  1  0  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
  9 14  1  0  0  0  0
 14 15  2  0  0  0  0
 13 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
 18 19  1  0  0  0  0
 18 20  1  0  0  0  0
 13 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  2  0  0  0  0
 23 24  1  0  0  0  0
 23 25  1  0  0  0  0
 12 26  1  0  0  0  0
 11 27  1  0  0  0  0
 28 27  1  6  0  0  0
 28 29  1  0  0  0  0
 29 30  1  0  0  0  0
 30 31  1  0  0  0  0
 31 32  1  0  0  0  0
 28 32  1  0  0  0  0
 32 33  1  1  0  0  0
 33 34  2  0  0  0  0
 33 35  1  0  0  0  0
 29 36  1  1  0  0  0
 29 37  1  6  0  0  0
 10 38  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0051726

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)=CCC1(CC=C(C)C)C(O)=C(C[C@@H]2[C@H](CC[C@]2(C)O)C(C)=C)C(O)=C(C(=O)C2=CC=CC=C2)C1=O

> <INCHI_IDENTIFIER>
InChI=1S/C33H42O5/c1-20(2)13-17-33(18-14-21(3)4)30(36)25(19-26-24(22(5)6)15-16-32(26,7)38)29(35)27(31(33)37)28(34)23-11-9-8-10-12-23/h8-14,24,26,35-36,38H,5,15-19H2,1-4,6-7H3/t24-,26-,32+/m1/s1

> <INCHI_KEY>
NTCBJJMOLYDOIE-OKQRBPQJSA-N

> <FORMULA>
C33H42O5

> <MOLECULAR_WEIGHT>
518.694

> <EXACT_MASS>
518.303224452

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
80

> <JCHEM_AVERAGE_POLARIZABILITY>
58.038527026959265

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-benzoyl-3,5-dihydroxy-4-{[(1R,2S,5S)-2-hydroxy-2-methyl-5-(prop-1-en-2-yl)cyclopentyl]methyl}-6,6-bis(3-methylbut-2-en-1-yl)cyclohexa-2,4-dien-1-one

> <ALOGPS_LOGP>
4.77

> <JCHEM_LOGP>
6.1408782806666675

> <ALOGPS_LOGS>
-4.96

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
7.956733654406662

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.460952154068138

> <JCHEM_PKA_STRONGEST_BASIC>
-0.6701688605513206

> <JCHEM_POLAR_SURFACE_AREA>
94.83000000000001

> <JCHEM_REFRACTIVITY>
156.75080000000005

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
5.68e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
hypercalin B

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  C   UNK     0      -2.692  -5.766   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -3.837  -4.736   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -3.517  -3.229   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -2.052  -2.753   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.907  -3.784   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -1.228  -5.290   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.723  -3.479   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       1.749  -4.737   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       0.877  -1.802   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -0.267  -0.771   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.053   0.735   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       1.518   1.211   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       2.662   0.181   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       2.342  -1.326   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       3.286  -2.633   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       3.115   1.781   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       3.193   3.437   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       4.307   4.698   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       5.836   5.172   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       4.140   6.303   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       4.383  -0.159   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       5.973   0.459   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       7.605   0.601   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       8.252  -0.840   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       8.941   1.538   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       1.846   2.836   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0      -1.074   1.871   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      -2.556   1.290   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      -3.802   2.195   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      -5.048   1.290   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      -4.572  -0.175   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      -3.032  -0.175   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      -2.462  -1.831   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      -2.475  -3.545   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      -0.573  -1.911   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      -4.915   3.401   0.000  0.00  0.00           C+0
HETATM   37  O   UNK     0      -3.112   3.682   0.000  0.00  0.00           O+0
HETATM   38  O   UNK     0      -1.557  -1.483   0.000  0.00  0.00           O+0
CONECT    1    2    6                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5    1                                                       
CONECT    7    5    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10   14                                                  
CONECT   10    9   11   38                                                  
CONECT   11   10   12   27                                                  
CONECT   12   11   13   26                                                  
CONECT   13   12   14   16   21                                             
CONECT   14   13    9   15                                                  
CONECT   15   14                                                            
CONECT   16   13   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18                                                            
CONECT   21   13   22                                                       
CONECT   22   21   23                                                       
CONECT   23   22   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23                                                            
CONECT   26   12                                                            
CONECT   27   11   28                                                       
CONECT   28   27   29   32                                                  
CONECT   29   28   30   36   37                                             
CONECT   30   29   31                                                       
CONECT   31   30   32                                                       
CONECT   32   31   28   33                                                  
CONECT   33   32   34   35                                                  
CONECT   34   33                                                            
CONECT   35   33                                                            
CONECT   36   29                                                            
CONECT   37   29                                                            
CONECT   38   10                                                            
MASTER        0    0    0    0    0    0    0    0   38    0   80    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₃₃H₄₂O₅

Average Mass

518.6940 Da

Monoisotopic Mass

518.30322 Da

IUPAC Name

2-benzoyl-3,5-dihydroxy-4-{[(1R,2S,5S)-2-hydroxy-2-methyl-5-(prop-1-en-2-yl)cyclopentyl]methyl}-6,6-bis(3-methylbut-2-en-1-yl)cyclohexa-2,4-dien-1-one

Traditional Name

hypercalin B

CAS Registry Number

Not Available

SMILES

CC(C)=CCC1(CC=C(C)C)C(O)=C(C[C@@H]2[C@H](CC[C@]2(C)O)C(C)=C)C(O)=C(C(=O)C2=CC=CC=C2)C1=O

InChI Identifier

InChI=1S/C33H42O5/c1-20(2)13-17-33(18-14-21(3)4)30(36)25(19-26-24(22(5)6)15-16-32(26,7)38)29(35)27(31(33)37)28(34)23-11-9-8-10-12-23/h8-14,24,26,35-36,38H,5,15-19H2,1-4,6-7H3/t24-,26-,32+/m1/s1

InChI Key

NTCBJJMOLYDOIE-OKQRBPQJSA-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 ascyron	Plant	KNApSAcK
Hypericum beanii	LOTUS Database	35616633
Hypericum calycinum	Plant	KNApSAcK
Hypericum calycunum	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as aromatic monoterpenoids. These are monoterpenoids containing at least one aromatic ring.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Monoterpenoids

Direct Parent

Aromatic monoterpenoids

Alternative Parents

Substituents

Aromatic monoterpenoid
Monocyclic monoterpenoid
Benzoyl
Aryl ketone
Benzenoid
Cyclopentanol
Monocyclic benzene moiety
Tertiary alcohol
Cyclic alcohol
Vinylogous acid
Cyclic ketone
Ketone
Enol
Organooxygen compound
Organic oxide
Carbonyl group
Alcohol
Organic oxygen compound
Hydrocarbon derivative
Aromatic homomonocyclic compound

Molecular Framework

Aromatic homomonocyclic compounds

External Descriptors

monoterpenoid (CHEBI:5833 )

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	4.77	ALOGPS
logP	6.14	ChemAxon
logS	-5	ALOGPS
pKa (Strongest Acidic)	4.46	ChemAxon
pKa (Strongest Basic)	-0.67	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	94.83 Å²	ChemAxon
Rotatable Bond Count	9	ChemAxon
Refractivity	156.75 m³·mol⁻¹	ChemAxon
Polarizability	58.04 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00002997

Chemspider ID

30791169

KEGG Compound ID

C09941

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

5833

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Hypercalin B (NP0051726)

MOL for NP0051726 (Hypercalin B)

3D MOL for NP0051726 (Hypercalin B)

3D SDF for NP0051726 (Hypercalin B)

3D-SDF for NP0051726 (Hypercalin B)

PDB for NP0051726 (Hypercalin B)

3D PDB for NP0051726 (Hypercalin B)

SMILES for NP0051726 (Hypercalin B)

INCHI for NP0051726 (Hypercalin B)

Structure for NP0051726 (Hypercalin B)

3D Structure for NP0051726 (Hypercalin B)