NP-MRD: Showing NP-Card for (2r)-2-[(1r,3ar,5ar,9as,11ar)-3a,6,6,9a,11a-pentamethyl-7-oxo-1h,2h,3h,5h,5ah,8h,9h,11h-cyclopenta[a]phenanthren-1-yl]-6-methyl-5-methylideneheptanoic acid (NP0314647)

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Record Information

Version

2.0

Created at

2022-09-11 12:51:01 UTC

Updated at

2022-09-11 12:51:02 UTC

NP-MRD ID

NP0314647

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2r)-2-[(1r,3ar,5ar,9as,11ar)-3a,6,6,9a,11a-pentamethyl-7-oxo-1h,2h,3h,5h,5ah,8h,9h,11h-cyclopenta[a]phenanthren-1-yl]-6-methyl-5-methylideneheptanoic acid

Description

Dehydroebriconic acid, also known as dehydroebriconate, belongs to the class of organic compounds known as ergosterols and derivatives. These are steroids containing ergosta-5,7,22-trien-3beta-ol or a derivative thereof, which is based on the 3beta-hydroxylated ergostane skeleton. (2r)-2-[(1r,3ar,5ar,9as,11ar)-3a,6,6,9a,11a-pentamethyl-7-oxo-1h,2h,3h,5h,5ah,8h,9h,11h-cyclopenta[a]phenanthren-1-yl]-6-methyl-5-methylideneheptanoic acid was first documented in 2004 (PMID: 15072595). Based on a literature review very few articles have been published on Dehydroebriconic acid.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309112214512D          

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M  END

     RDKit          3D

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M  END


  Mrv1652309112214512D          

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    7.8503   -2.4430    0.0000 C   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  1  0  0  0  0
  5  4  1  1  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  6  8  1  0  0  0  0
  9  5  1  1  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  6  0  0  0
 12 14  1  0  0  0  0
 14 15  2  0  0  0  0
 15 16  1  0  0  0  0
 17 16  1  1  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 18 20  1  0  0  0  0
 18 21  1  0  0  0  0
 21 22  2  0  0  0  0
 21 23  1  0  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 17 25  1  0  0  0  0
 25 26  1  1  0  0  0
 25 27  1  0  0  0  0
 14 27  1  0  0  0  0
 27 28  2  0  0  0  0
 28 29  1  0  0  0  0
 29 30  1  0  0  0  0
  9 30  1  0  0  0  0
 12 30  1  0  0  0  0
 30 31  1  1  0  0  0
  2 32  1  0  0  0  0
 32 33  1  0  0  0  0
 32 34  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0314647

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)C(=C)CC[C@H]([C@H]1CC[C@@]2(C)C3=CC[C@H]4C(C)(C)C(=O)CC[C@]4(C)C3=CC[C@]12C)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C31H46O3/c1-19(2)20(3)9-10-21(27(33)34)22-13-17-31(8)24-11-12-25-28(4,5)26(32)15-16-29(25,6)23(24)14-18-30(22,31)7/h11,14,19,21-22,25H,3,9-10,12-13,15-18H2,1-2,4-8H3,(H,33,34)/t21-,22-,25+,29-,30-,31+/m1/s1

> <INCHI_KEY>
DVXFDXIVWQWLIU-DIQRFASRSA-N

> <FORMULA>
C31H46O3

> <MOLECULAR_WEIGHT>
466.706

> <EXACT_MASS>
466.344695341

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
80

> <JCHEM_AVERAGE_POLARIZABILITY>
56.12973477089552

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R)-6-methyl-5-methylidene-2-[(2S,7R,11R,14R,15R)-2,6,6,11,15-pentamethyl-5-oxotetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadeca-1(17),9-dien-14-yl]heptanoic acid

> <JCHEM_LOGP>
7.188956753666667

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
19.63519884633931

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.849380622473484

> <JCHEM_PKA_STRONGEST_BASIC>
-7.471493604954322

> <JCHEM_POLAR_SURFACE_AREA>
54.37

> <JCHEM_REFRACTIVITY>
140.00639999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(2R)-6-methyl-5-methylidene-2-[(2S,7R,11R,14R,15R)-2,6,6,11,15-pentamethyl-5-oxotetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadeca-1(17),9-dien-14-yl]heptanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 11-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-22         0                                  
HETATM    1  C   UNK     0      13.320  -0.710   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      13.320  -2.250   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      11.987  -3.020   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      10.653  -2.250   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       9.319  -3.020   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       9.319  -4.560   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      10.653  -5.330   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       7.986  -5.330   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       7.986  -2.250   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       6.579  -2.877   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       5.548  -1.732   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       6.318  -0.399   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       4.787  -0.238   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       5.842   1.066   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       4.336   1.386   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       3.860   2.851   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       4.891   3.995   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       4.415   5.460   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       3.055   4.737   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       3.467   6.674   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       5.445   6.604   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       4.969   8.069   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0       6.951   6.284   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       7.427   4.820   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       6.397   3.675   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       7.903   3.355   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       6.873   2.211   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       8.379   1.890   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       8.855   0.426   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       7.825  -0.719   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       9.289  -1.195   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      14.654  -3.020   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      15.988  -2.250   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      14.654  -4.560   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   32                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6    9                                                  
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6                                                            
CONECT    9    5   10   30                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13   14   30                                             
CONECT   13   12                                                            
CONECT   14   12   15   27                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18   25                                                  
CONECT   18   17   19   20   21                                             
CONECT   19   18                                                            
CONECT   20   18                                                            
CONECT   21   18   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24   17   26   27                                             
CONECT   26   25                                                            
CONECT   27   25   14   28                                                  
CONECT   28   27   29                                                       
CONECT   29   28   30                                                       
CONECT   30   29    9   12   31                                             
CONECT   31   30                                                            
CONECT   32    2   33   34                                                  
CONECT   33   32                                                            
CONECT   34   32                                                            
MASTER        0    0    0    0    0    0    0    0   34    0   74    0
END

View in JSmol

Synonyms

Value	Source
Dehydroebriconate	Generator

Chemical Formula

C₃₁H₄₆O₃

Average Mass

466.7060 Da

Monoisotopic Mass

466.34470 Da

IUPAC Name

(2R)-6-methyl-5-methylidene-2-[(2S,7R,11R,14R,15R)-2,6,6,11,15-pentamethyl-5-oxotetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadeca-1(17),9-dien-14-yl]heptanoic acid

Traditional Name

(2R)-6-methyl-5-methylidene-2-[(2S,7R,11R,14R,15R)-2,6,6,11,15-pentamethyl-5-oxotetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadeca-1(17),9-dien-14-yl]heptanoic acid

CAS Registry Number

Not Available

SMILES

CC(C)C(=C)CC[C@H]([C@H]1CC[C@@]2(C)C3=CC[C@H]4C(C)(C)C(=O)CC[C@]4(C)C3=CC[C@]12C)C(O)=O

InChI Identifier

InChI=1S/C31H46O3/c1-19(2)20(3)9-10-21(27(33)34)22-13-17-31(8)24-11-12-25-28(4,5)26(32)15-16-29(25,6)23(24)14-18-30(22,31)7/h11,14,19,21-22,25H,3,9-10,12-13,15-18H2,1-2,4-8H3,(H,33,34)/t21-,22-,25+,29-,30-,31+/m1/s1

InChI Key

DVXFDXIVWQWLIU-DIQRFASRSA-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

Not Available

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as ergosterols and derivatives. These are steroids containing ergosta-5,7,22-trien-3beta-ol or a derivative thereof, which is based on the 3beta-hydroxylated ergostane skeleton.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Steroids and steroid derivatives

Sub Class

Ergostane steroids

Direct Parent

Ergosterols and derivatives

Alternative Parents

Substituents

Triterpenoid
Ergosterol-skeleton
Bile acid, alcohol, or derivatives
Steroid acid
3-oxo-delta-7-steroid
3-oxosteroid
14-alpha-methylsteroid
3-oxo-5-alpha-steroid
Oxosteroid
Delta-7-steroid
Medium-chain fatty acid
Fatty acyl
Fatty acid
Unsaturated fatty acid
Cyclic ketone
Ketone
Carboxylic acid
Carboxylic acid derivative
Monocarboxylic acid or derivatives
Organooxygen compound
Organic oxygen compound
Carbonyl group
Hydrocarbon derivative
Organic oxide
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	7.19	ChemAxon
pKa (Strongest Acidic)	4.85	ChemAxon
pKa (Strongest Basic)	-7.5	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	54.37 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	140.01 m³·mol⁻¹	ChemAxon
Polarizability	56.13 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	Yes	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

Not Available

Chemspider ID

32762855

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

24202864

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Mizushina Y, Akihisa T, Ukiya M, Murakami C, Kuriyama I, Xu X, Yoshida H, Sakaguchi K: A novel DNA topoisomerase inhibitor: dehydroebriconic acid, one of the lanostane-type triterpene acids from Poria cocos. Cancer Sci. 2004 Apr;95(4):354-60. doi: 10.1111/j.1349-7006.2004.tb03215.x. [PubMed:15072595 ]
LOTUS database [Link]

Showing NP-Card for (2r)-2-[(1r,3ar,5ar,9as,11ar)-3a,6,6,9a,11a-pentamethyl-7-oxo-1h,2h,3h,5h,5ah,8h,9h,11h-cyclopenta[a]phenanthren-1-yl]-6-methyl-5-methylideneheptanoic acid (NP0314647)

MOL for NP0314647 ((2r)-2-[(1r,3ar,5ar,9as,11ar)-3a,6,6,9a,11a-pentamethyl-7-oxo-1h,2h,3h,5h,5ah,8h,9h,11h-cyclopenta[a]phenanthren-1-yl]-6-methyl-5-methylideneheptanoic acid)

3D MOL for NP0314647 ((2r)-2-[(1r,3ar,5ar,9as,11ar)-3a,6,6,9a,11a-pentamethyl-7-oxo-1h,2h,3h,5h,5ah,8h,9h,11h-cyclopenta[a]phenanthren-1-yl]-6-methyl-5-methylideneheptanoic acid)

3D SDF for NP0314647 ((2r)-2-[(1r,3ar,5ar,9as,11ar)-3a,6,6,9a,11a-pentamethyl-7-oxo-1h,2h,3h,5h,5ah,8h,9h,11h-cyclopenta[a]phenanthren-1-yl]-6-methyl-5-methylideneheptanoic acid)

3D-SDF for NP0314647 ((2r)-2-[(1r,3ar,5ar,9as,11ar)-3a,6,6,9a,11a-pentamethyl-7-oxo-1h,2h,3h,5h,5ah,8h,9h,11h-cyclopenta[a]phenanthren-1-yl]-6-methyl-5-methylideneheptanoic acid)

PDB for NP0314647 ((2r)-2-[(1r,3ar,5ar,9as,11ar)-3a,6,6,9a,11a-pentamethyl-7-oxo-1h,2h,3h,5h,5ah,8h,9h,11h-cyclopenta[a]phenanthren-1-yl]-6-methyl-5-methylideneheptanoic acid)

3D PDB for NP0314647 ((2r)-2-[(1r,3ar,5ar,9as,11ar)-3a,6,6,9a,11a-pentamethyl-7-oxo-1h,2h,3h,5h,5ah,8h,9h,11h-cyclopenta[a]phenanthren-1-yl]-6-methyl-5-methylideneheptanoic acid)

SMILES for NP0314647 ((2r)-2-[(1r,3ar,5ar,9as,11ar)-3a,6,6,9a,11a-pentamethyl-7-oxo-1h,2h,3h,5h,5ah,8h,9h,11h-cyclopenta[a]phenanthren-1-yl]-6-methyl-5-methylideneheptanoic acid)

INCHI for NP0314647 ((2r)-2-[(1r,3ar,5ar,9as,11ar)-3a,6,6,9a,11a-pentamethyl-7-oxo-1h,2h,3h,5h,5ah,8h,9h,11h-cyclopenta[a]phenanthren-1-yl]-6-methyl-5-methylideneheptanoic acid)

Structure for NP0314647 ((2r)-2-[(1r,3ar,5ar,9as,11ar)-3a,6,6,9a,11a-pentamethyl-7-oxo-1h,2h,3h,5h,5ah,8h,9h,11h-cyclopenta[a]phenanthren-1-yl]-6-methyl-5-methylideneheptanoic acid)

3D Structure for NP0314647 ((2r)-2-[(1r,3ar,5ar,9as,11ar)-3a,6,6,9a,11a-pentamethyl-7-oxo-1h,2h,3h,5h,5ah,8h,9h,11h-cyclopenta[a]phenanthren-1-yl]-6-methyl-5-methylideneheptanoic acid)