NP-MRD: Showing NP-Card for 3a,6,6,9a,11a-pentamethyl-1-(5,6,7-trihydroxy-6-methylheptan-2-yl)-1h,2h,3h,5h,5ah,8h,9h,10h,11h-cyclopenta[a]phenanthrene-4,7-dione (NP0145237)

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Record Information

Version

2.0

Created at

2022-09-02 00:23:41 UTC

Updated at

2022-09-02 00:23:41 UTC

NP-MRD ID

NP0145237

Secondary Accession Numbers

None

Natural Product Identification

Common Name

3a,6,6,9a,11a-pentamethyl-1-(5,6,7-trihydroxy-6-methylheptan-2-yl)-1h,2h,3h,5h,5ah,8h,9h,10h,11h-cyclopenta[a]phenanthrene-4,7-dione

Description

Ganoderiol D belongs to the class of organic compounds known as triterpenoids. These are terpene molecules containing six isoprene units. Ganoderiol D is an extremely weak basic (essentially neutral) compound (based on its pKa). Outside of the human body, ganoderiol D has been detected, but not quantified in, mushrooms. 3a,6,6,9a,11a-pentamethyl-1-(5,6,7-trihydroxy-6-methylheptan-2-yl)-1h,2h,3h,5h,5ah,8h,9h,10h,11h-cyclopenta[a]phenanthrene-4,7-dione is found in Ganoderma sinense. This could make ganoderiol D a potential biomarker for the consumption of these foods.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv0541 05061310012D          

 35 38  0  0  0  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv0541 05061310012D          

 35 38  0  0  0  0            999 V2000
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    3.4587   -0.5029    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7998   -2.9803    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1234   -3.5188    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0193    1.0490    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.0511   -0.4075    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6043   -1.5648    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1484   -3.4866    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  9  8  1  0  0  0  0
 13 12  1  0  0  0  0
 14 11  1  0  0  0  0
 15 10  1  0  0  0  0
 18  1  1  0  0  0  0
 18  8  1  0  0  0  0
 19 10  1  0  0  0  0
 19 18  1  0  0  0  0
 20 11  1  0  0  0  0
 21 16  1  0  0  0  0
 22 16  1  0  0  0  0
 23 12  1  0  0  0  0
 24  9  1  0  0  0  0
 25 20  2  0  0  0  0
 25 21  1  0  0  0  0
 26  2  1  0  0  0  0
 26  3  1  0  0  0  0
 26 22  1  0  0  0  0
 26 23  1  0  0  0  0
 27  4  1  0  0  0  0
 27 13  1  0  0  0  0
 27 20  1  0  0  0  0
 27 22  1  0  0  0  0
 28  5  1  0  0  0  0
 28 14  1  0  0  0  0
 28 19  1  0  0  0  0
 29  6  1  0  0  0  0
 29 15  1  0  0  0  0
 29 25  1  0  0  0  0
 29 28  1  0  0  0  0
 30  7  1  0  0  0  0
 30 17  1  0  0  0  0
 30 24  1  0  0  0  0
 31 17  1  0  0  0  0
 32 21  2  0  0  0  0
 33 23  2  0  0  0  0
 34 24  1  0  0  0  0
 35 30  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0145237

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(CCC(O)C(C)(O)CO)C1CCC2(C)C3=C(CCC12C)C1(C)CCC(=O)C(C)(C)C1CC3=O

> <INCHI_IDENTIFIER>
InChI=1S/C30H48O5/c1-18(8-9-24(34)30(7,35)17-31)19-10-15-29(6)25-20(11-14-28(19,29)5)27(4)13-12-23(33)26(2,3)22(27)16-21(25)32/h18-19,22,24,31,34-35H,8-17H2,1-7H3

> <INCHI_KEY>
NAETYGPWGSNZTO-UHFFFAOYSA-N

> <FORMULA>
C30H48O5

> <MOLECULAR_WEIGHT>
488.6991

> <EXACT_MASS>
488.350174646

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
57.49028525658255

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2,6,6,11,15-pentamethyl-14-(5,6,7-trihydroxy-6-methylheptan-2-yl)tetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadec-1(10)-ene-5,9-dione

> <ALOGPS_LOGP>
4.88

> <JCHEM_LOGP>
4.415568088000001

> <ALOGPS_LOGS>
-5.08

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.579262063881586

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.189670921843057

> <JCHEM_PKA_STRONGEST_BASIC>
-3.1028507388909476

> <JCHEM_POLAR_SURFACE_AREA>
94.83

> <JCHEM_REFRACTIVITY>
138.30689999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.08e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2,6,6,11,15-pentamethyl-14-(5,6,7-trihydroxy-6-methylheptan-2-yl)tetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadec-1(10)-ene-5,9-dione

> <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       4.029  -4.979   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      11.990   1.591   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      13.852   0.919   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       9.958  -3.022   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       5.261  -3.773   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.825   0.556   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -2.709  -4.618   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.923  -3.342   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.978  -4.558   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       3.966  -0.858   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       8.442  -3.293   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      12.990  -2.480   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      11.473  -2.751   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       6.926  -3.564   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       5.240   0.007   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      10.011   1.052   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -2.438  -6.779   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       3.448  -3.553   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       4.394  -2.337   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       8.965  -1.845   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       8.495   0.781   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      11.004  -0.125   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      13.513  -1.032   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -0.548  -4.347   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       7.972  -0.668   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      12.520   0.146   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      10.481  -1.574   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       5.933  -2.387   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       6.456  -0.939   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      -1.493  -5.563   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0      -3.964  -6.568   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0       7.503   1.958   0.000  0.00  0.00           O+0
HETATM   33  O   UNK     0      15.029  -0.761   0.000  0.00  0.00           O+0
HETATM   34  O   UNK     0      -1.128  -2.921   0.000  0.00  0.00           O+0
HETATM   35  O   UNK     0      -0.277  -6.508   0.000  0.00  0.00           O+0
CONECT    1   18                                                            
CONECT    2   26                                                            
CONECT    3   26                                                            
CONECT    4   27                                                            
CONECT    5   28                                                            
CONECT    6   29                                                            
CONECT    7   30                                                            
CONECT    8    9   18                                                       
CONECT    9    8   24                                                       
CONECT   10   15   19                                                       
CONECT   11   14   20                                                       
CONECT   12   13   23                                                       
CONECT   13   12   27                                                       
CONECT   14   11   28                                                       
CONECT   15   10   29                                                       
CONECT   16   21   22                                                       
CONECT   17   30   31                                                       
CONECT   18    1    8   19                                                  
CONECT   19   10   18   28                                                  
CONECT   20   11   25   27                                                  
CONECT   21   16   25   32                                                  
CONECT   22   16   26   27                                                  
CONECT   23   12   26   33                                                  
CONECT   24    9   30   34                                                  
CONECT   25   20   21   29                                                  
CONECT   26    2    3   22   23                                             
CONECT   27    4   13   20   22                                             
CONECT   28    5   14   19   29                                             
CONECT   29    6   15   25   28                                             
CONECT   30    7   17   24   35                                             
CONECT   31   17                                                            
CONECT   32   21                                                            
CONECT   33   23                                                            
CONECT   34   24                                                            
CONECT   35   30                                                            
MASTER        0    0    0    0    0    0    0    0   35    0   76    0
END

View in JSmol

Synonyms

Value	Source
24,25,26-Tetrahydroxy-8-lanostene-3,7-dione	HMDB

Chemical Formula

C₃₀H₄₈O₅

Average Mass

488.6991 Da

Monoisotopic Mass

488.35017 Da

IUPAC Name

2,6,6,11,15-pentamethyl-14-(5,6,7-trihydroxy-6-methylheptan-2-yl)tetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadec-1(10)-ene-5,9-dione

Traditional Name

2,6,6,11,15-pentamethyl-14-(5,6,7-trihydroxy-6-methylheptan-2-yl)tetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadec-1(10)-ene-5,9-dione

CAS Registry Number

Not Available

SMILES

CC(CCC(O)C(C)(O)CO)C1CCC2(C)C3=C(CCC12C)C1(C)CCC(=O)C(C)(C)C1CC3=O

InChI Identifier

InChI=1S/C30H48O5/c1-18(8-9-24(34)30(7,35)17-31)19-10-15-29(6)25-20(11-14-28(19,29)5)27(4)13-12-23(33)26(2,3)22(27)16-21(25)32/h18-19,22,24,31,34-35H,8-17H2,1-7H3

InChI Key

NAETYGPWGSNZTO-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
Ganoderma sinense	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as triterpenoids. These are terpene molecules containing six isoprene units.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Triterpenoids

Direct Parent

Triterpenoids

Alternative Parents

Not Available

Substituents

Not Available

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	4.88	ALOGPS
logP	4.42	ChemAxon
logS	-5.1	ALOGPS
pKa (Strongest Acidic)	13.19	ChemAxon
pKa (Strongest Basic)	-3.1	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	94.83 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	138.31 m³·mol⁻¹	ChemAxon
Polarizability	57.49 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

External Links

HMDB ID

HMDB0037782

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB016924

KNApSAcK ID

C00023860

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

15602261

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 3a,6,6,9a,11a-pentamethyl-1-(5,6,7-trihydroxy-6-methylheptan-2-yl)-1h,2h,3h,5h,5ah,8h,9h,10h,11h-cyclopenta[a]phenanthrene-4,7-dione (NP0145237)

MOL for NP0145237 (3a,6,6,9a,11a-pentamethyl-1-(5,6,7-trihydroxy-6-methylheptan-2-yl)-1h,2h,3h,5h,5ah,8h,9h,10h,11h-cyclopenta[a]phenanthrene-4,7-dione)

3D MOL for NP0145237 (3a,6,6,9a,11a-pentamethyl-1-(5,6,7-trihydroxy-6-methylheptan-2-yl)-1h,2h,3h,5h,5ah,8h,9h,10h,11h-cyclopenta[a]phenanthrene-4,7-dione)

3D SDF for NP0145237 (3a,6,6,9a,11a-pentamethyl-1-(5,6,7-trihydroxy-6-methylheptan-2-yl)-1h,2h,3h,5h,5ah,8h,9h,10h,11h-cyclopenta[a]phenanthrene-4,7-dione)

3D-SDF for NP0145237 (3a,6,6,9a,11a-pentamethyl-1-(5,6,7-trihydroxy-6-methylheptan-2-yl)-1h,2h,3h,5h,5ah,8h,9h,10h,11h-cyclopenta[a]phenanthrene-4,7-dione)

PDB for NP0145237 (3a,6,6,9a,11a-pentamethyl-1-(5,6,7-trihydroxy-6-methylheptan-2-yl)-1h,2h,3h,5h,5ah,8h,9h,10h,11h-cyclopenta[a]phenanthrene-4,7-dione)

3D PDB for NP0145237 (3a,6,6,9a,11a-pentamethyl-1-(5,6,7-trihydroxy-6-methylheptan-2-yl)-1h,2h,3h,5h,5ah,8h,9h,10h,11h-cyclopenta[a]phenanthrene-4,7-dione)

SMILES for NP0145237 (3a,6,6,9a,11a-pentamethyl-1-(5,6,7-trihydroxy-6-methylheptan-2-yl)-1h,2h,3h,5h,5ah,8h,9h,10h,11h-cyclopenta[a]phenanthrene-4,7-dione)

INCHI for NP0145237 (3a,6,6,9a,11a-pentamethyl-1-(5,6,7-trihydroxy-6-methylheptan-2-yl)-1h,2h,3h,5h,5ah,8h,9h,10h,11h-cyclopenta[a]phenanthrene-4,7-dione)

Structure for NP0145237 (3a,6,6,9a,11a-pentamethyl-1-(5,6,7-trihydroxy-6-methylheptan-2-yl)-1h,2h,3h,5h,5ah,8h,9h,10h,11h-cyclopenta[a]phenanthrene-4,7-dione)

3D Structure for NP0145237 (3a,6,6,9a,11a-pentamethyl-1-(5,6,7-trihydroxy-6-methylheptan-2-yl)-1h,2h,3h,5h,5ah,8h,9h,10h,11h-cyclopenta[a]phenanthrene-4,7-dione)