NP-MRD: Showing NP-Card for 7-[1-(4,5-dimethyl-6-oxo-2,3-dihydropyran-2-yl)-1-hydroxyethyl]-7,16,17-trihydroxy-8,12-dimethyl-18-oxapentacyclo[13.2.1.0³,¹¹.0⁴,⁸.0¹²,¹⁷]octadec-4-en-13-one (NP0203653)

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Record Information

Version

2.0

Created at

2022-09-04 23:10:04 UTC

Updated at

2022-09-04 23:10:04 UTC

NP-MRD ID

NP0203653

Secondary Accession Numbers

None

Natural Product Identification

Common Name

7-[1-(4,5-dimethyl-6-oxo-2,3-dihydropyran-2-yl)-1-hydroxyethyl]-7,16,17-trihydroxy-8,12-dimethyl-18-oxapentacyclo[13.2.1.0³,¹¹.0⁴,⁸.0¹²,¹⁷]octadec-4-en-13-one

Description

Barogenin, also known as kryptogenin, belongs to the class of organic compounds known as dihydroxy bile acids, alcohols and derivatives. Dihydroxy bile acids, alcohols and derivatives are compounds containing or derived from a bile acid or alcohol, and which bears exactly two carboxylic acid groups. 7-[1-(4,5-dimethyl-6-oxo-2,3-dihydropyran-2-yl)-1-hydroxyethyl]-7,16,17-trihydroxy-8,12-dimethyl-18-oxapentacyclo[13.2.1.0³,¹¹.0⁴,⁸.0¹²,¹⁷]octadec-4-en-13-one is found in Physalis peruviana. Barogenin is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv0541 02241219192D          

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M  END

     RDKit          3D

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M  END


  Mrv0541 02241219192D          

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  2 27  1  0  0  0  0
  3  4  1  0  0  0  0
  3 28  1  0  0  0  0
  4  5  1  0  0  0  0
  4 33  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  7 29  1  0  0  0  0
  7 32  1  0  0  0  0
  8  9  1  0  0  0  0
  8 12  1  0  0  0  0
  8 34  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 11 12  1  0  0  0  0
 11 16  1  0  0  0  0
 12 13  1  0  0  0  0
 12 30  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 15 23  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 18 24  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 20 25  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 22 35  2  0  0  0  0
 23 24  1  0  0  0  0
 23 31  1  0  0  0  0
 24 25  1  0  0  0  0
 24 36  1  0  0  0  0
 25 26  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0203653

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC1=C(C)C(=O)OC(C1)C(C)(O)C1(O)CC=C2C3CC4OC5CC(=O)C(C)(C3CCC12C)C4(O)C5O

> <INCHI_IDENTIFIER>
InChI=1S/C28H38O8/c1-13-10-20(36-23(31)14(13)2)26(5,32)27(33)9-7-16-15-11-21-28(34)22(30)18(35-21)12-19(29)25(28,4)17(15)6-8-24(16,27)3/h7,15,17-18,20-22,30,32-34H,6,8-12H2,1-5H3

> <INCHI_KEY>
YZKXYOSYQKJNOD-UHFFFAOYSA-N

> <FORMULA>
C28H38O8

> <MOLECULAR_WEIGHT>
502.5965

> <EXACT_MASS>
502.256668192

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_AVERAGE_POLARIZABILITY>
54.244644274707184

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
7-[1-(4,5-dimethyl-6-oxo-3,6-dihydro-2H-pyran-2-yl)-1-hydroxyethyl]-7,16,17-trihydroxy-8,12-dimethyl-18-oxapentacyclo[13.2.1.0³,¹¹.0⁴,⁸.0¹²,¹⁷]octadec-4-en-13-one

> <ALOGPS_LOGP>
1.46

> <JCHEM_LOGP>
1.377654083

> <ALOGPS_LOGS>
-3.10

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.797151425777969

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.119656362363411

> <JCHEM_PKA_STRONGEST_BASIC>
-3.6076774642386438

> <JCHEM_POLAR_SURFACE_AREA>
133.52

> <JCHEM_REFRACTIVITY>
129.2864

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
4.02e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
7-[1-(4,5-dimethyl-6-oxo-2,3-dihydropyran-2-yl)-1-hydroxyethyl]-7,16,17-trihydroxy-8,12-dimethyl-18-oxapentacyclo[13.2.1.0³,¹¹.0⁴,⁸.0¹²,¹⁷]octadec-4-en-13-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0      -5.236  -0.673   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -6.733  -0.523   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -7.331   0.972   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -6.434   2.169   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      -4.938   2.020   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      -4.189   0.673   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -2.693   0.374   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -1.047   0.225   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -1.047   1.720   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.450   2.169   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.345   0.972   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.450  -0.223   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       1.345  -1.571   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       2.693  -1.571   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       3.741  -0.374   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       2.842   0.972   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       3.741   2.169   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       5.236   1.869   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       8.379   3.515   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       8.379  -0.972   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       7.631  -2.319   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       5.985  -2.169   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       5.236  -0.673   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       6.134   0.673   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       7.631   0.374   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       8.828   1.421   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0      -7.631  -1.720   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      -8.828   1.122   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      -3.291  -0.972   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       0.150  -1.869   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       4.488  -2.020   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0      -2.842   2.020   0.000  0.00  0.00           O+0
HETATM   33  O   UNK     0      -7.033   3.666   0.000  0.00  0.00           O+0
HETATM   34  O   UNK     0      -1.496  -1.271   0.000  0.00  0.00           O+0
HETATM   35  O   UNK     0       5.536  -3.666   0.000  0.00  0.00           O+0
HETATM   36  O   UNK     0       6.733   2.020   0.000  0.00  0.00           O+0
CONECT    1    2    6                                                       
CONECT    2    1    3   27                                                  
CONECT    3    2    4   28                                                  
CONECT    4    3    5   33                                                  
CONECT    5    4    6                                                       
CONECT    6    1    5    7                                                  
CONECT    7    6    8   29   32                                             
CONECT    8    7    9   12   34                                             
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   16                                                  
CONECT   12    8   11   13   30                                             
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16   23                                                  
CONECT   16   11   15   17                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19   24                                                  
CONECT   19   18   20                                                       
CONECT   20   19   21   25                                                  
CONECT   21   20   22                                                       
CONECT   22   21   23   35                                                  
CONECT   23   15   22   24   31                                             
CONECT   24   18   23   25   36                                             
CONECT   25   20   24   26                                                  
CONECT   26   25                                                            
CONECT   27    2                                                            
CONECT   28    3                                                            
CONECT   29    7                                                            
CONECT   30   12                                                            
CONECT   31   23                                                            
CONECT   32    7                                                            
CONECT   33    4                                                            
CONECT   34    8                                                            
CONECT   35   22                                                            
CONECT   36   24                                                            
MASTER        0    0    0    0    0    0    0    0   36    0   82    0
END

View in JSmol

Synonyms

Value	Source
Kryptogenin	MeSH
3a,6a-Epoxy-4b,5,17b,20R-tetrahydroxy-1-oxo-5b,22R-witha-14,24-dienolide	HMDB

Chemical Formula

C₂₈H₃₈O₈

Average Mass

502.5965 Da

Monoisotopic Mass

502.25667 Da

IUPAC Name

7-[1-(4,5-dimethyl-6-oxo-3,6-dihydro-2H-pyran-2-yl)-1-hydroxyethyl]-7,16,17-trihydroxy-8,12-dimethyl-18-oxapentacyclo[13.2.1.0³,¹¹.0⁴,⁸.0¹²,¹⁷]octadec-4-en-13-one

Traditional Name

7-[1-(4,5-dimethyl-6-oxo-2,3-dihydropyran-2-yl)-1-hydroxyethyl]-7,16,17-trihydroxy-8,12-dimethyl-18-oxapentacyclo[13.2.1.0³,¹¹.0⁴,⁸.0¹²,¹⁷]octadec-4-en-13-one

CAS Registry Number

Not Available

SMILES

CC1=C(C)C(=O)OC(C1)C(C)(O)C1(O)CC=C2C3CC4OC5CC(=O)C(C)(C3CCC12C)C4(O)C5O

InChI Identifier

InChI=1S/C28H38O8/c1-13-10-20(36-23(31)14(13)2)26(5,32)27(33)9-7-16-15-11-21-28(34)22(30)18(35-21)12-19(29)25(28,4)17(15)6-8-24(16,27)3/h7,15,17-18,20-22,30,32-34H,6,8-12H2,1-5H3

InChI Key

YZKXYOSYQKJNOD-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, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, 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
Physalis peruviana	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as dihydroxy bile acids, alcohols and derivatives. Dihydroxy bile acids, alcohols and derivatives are compounds containing or derived from a bile acid or alcohol, and which bears exactly two carboxylic acid groups.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Steroids and steroid derivatives

Sub Class

Bile acids, alcohols and derivatives

Direct Parent

Dihydroxy bile acids, alcohols and derivatives

Alternative Parents

Substituents

26-hydroxysteroid
Dihydroxy bile acid, alcohol, or derivatives
22-oxosteroid
21-oxosteroid
3-hydroxy-delta-5-steroid
3-hydroxysteroid
Oxosteroid
16-oxosteroid
Hydroxysteroid
Delta-5-steroid
Fatty alcohol
Fatty acyl
Cyclic alcohol
Cyclic ketone
Secondary alcohol
Ketone
Organic oxide
Organic oxygen compound
Hydrocarbon derivative
Carbonyl group
Primary alcohol
Organooxygen compound
Alcohol
Aliphatic homopolycyclic compound

Molecular Framework

Aliphatic 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	1.46	ALOGPS
logP	1.38	ChemAxon
logS	-3.1	ALOGPS
pKa (Strongest Acidic)	12.12	ChemAxon
pKa (Strongest Basic)	-3.6	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	133.52 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	129.29 m³·mol⁻¹	ChemAxon
Polarizability	54.24 Å³	ChemAxon
Number of Rings	6	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

HMDB0034403

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB012807

KNApSAcK ID

Not Available

Chemspider ID

91878

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

101688

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 7-[1-(4,5-dimethyl-6-oxo-2,3-dihydropyran-2-yl)-1-hydroxyethyl]-7,16,17-trihydroxy-8,12-dimethyl-18-oxapentacyclo[13.2.1.0³,¹¹.0⁴,⁸.0¹²,¹⁷]octadec-4-en-13-one (NP0203653)

MOL for NP0203653 (7-[1-(4,5-dimethyl-6-oxo-2,3-dihydropyran-2-yl)-1-hydroxyethyl]-7,16,17-trihydroxy-8,12-dimethyl-18-oxapentacyclo[13.2.1.0³,¹¹.0⁴,⁸.0¹²,¹⁷]octadec-4-en-13-one)

3D MOL for NP0203653 (7-[1-(4,5-dimethyl-6-oxo-2,3-dihydropyran-2-yl)-1-hydroxyethyl]-7,16,17-trihydroxy-8,12-dimethyl-18-oxapentacyclo[13.2.1.0³,¹¹.0⁴,⁸.0¹²,¹⁷]octadec-4-en-13-one)

3D SDF for NP0203653 (7-[1-(4,5-dimethyl-6-oxo-2,3-dihydropyran-2-yl)-1-hydroxyethyl]-7,16,17-trihydroxy-8,12-dimethyl-18-oxapentacyclo[13.2.1.0³,¹¹.0⁴,⁸.0¹²,¹⁷]octadec-4-en-13-one)

3D-SDF for NP0203653 (7-[1-(4,5-dimethyl-6-oxo-2,3-dihydropyran-2-yl)-1-hydroxyethyl]-7,16,17-trihydroxy-8,12-dimethyl-18-oxapentacyclo[13.2.1.0³,¹¹.0⁴,⁸.0¹²,¹⁷]octadec-4-en-13-one)

PDB for NP0203653 (7-[1-(4,5-dimethyl-6-oxo-2,3-dihydropyran-2-yl)-1-hydroxyethyl]-7,16,17-trihydroxy-8,12-dimethyl-18-oxapentacyclo[13.2.1.0³,¹¹.0⁴,⁸.0¹²,¹⁷]octadec-4-en-13-one)

3D PDB for NP0203653 (7-[1-(4,5-dimethyl-6-oxo-2,3-dihydropyran-2-yl)-1-hydroxyethyl]-7,16,17-trihydroxy-8,12-dimethyl-18-oxapentacyclo[13.2.1.0³,¹¹.0⁴,⁸.0¹²,¹⁷]octadec-4-en-13-one)

SMILES for NP0203653 (7-[1-(4,5-dimethyl-6-oxo-2,3-dihydropyran-2-yl)-1-hydroxyethyl]-7,16,17-trihydroxy-8,12-dimethyl-18-oxapentacyclo[13.2.1.0³,¹¹.0⁴,⁸.0¹²,¹⁷]octadec-4-en-13-one)

INCHI for NP0203653 (7-[1-(4,5-dimethyl-6-oxo-2,3-dihydropyran-2-yl)-1-hydroxyethyl]-7,16,17-trihydroxy-8,12-dimethyl-18-oxapentacyclo[13.2.1.0³,¹¹.0⁴,⁸.0¹²,¹⁷]octadec-4-en-13-one)

Structure for NP0203653 (7-[1-(4,5-dimethyl-6-oxo-2,3-dihydropyran-2-yl)-1-hydroxyethyl]-7,16,17-trihydroxy-8,12-dimethyl-18-oxapentacyclo[13.2.1.0³,¹¹.0⁴,⁸.0¹²,¹⁷]octadec-4-en-13-one)

3D Structure for NP0203653 (7-[1-(4,5-dimethyl-6-oxo-2,3-dihydropyran-2-yl)-1-hydroxyethyl]-7,16,17-trihydroxy-8,12-dimethyl-18-oxapentacyclo[13.2.1.0³,¹¹.0⁴,⁸.0¹²,¹⁷]octadec-4-en-13-one)