NP-MRD: Showing NP-Card for (2e,6r)-6-[(1r,3as,3br,7s,9as,9br,11ar)-7-hydroxy-3a,6,6,9b,11a-pentamethyl-1h,2h,3h,3bh,4h,7h,8h,9h,9ah,10h,11h-cyclopenta[a]phenanthren-1-yl]-2-methylhept-2-enoic acid (NP0209052)

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Record Information

Version

2.0

Created at

2022-09-05 06:18:32 UTC

Updated at

2022-09-05 06:18:33 UTC

NP-MRD ID

NP0209052

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2e,6r)-6-[(1r,3as,3br,7s,9as,9br,11ar)-7-hydroxy-3a,6,6,9b,11a-pentamethyl-1h,2h,3h,3bh,4h,7h,8h,9h,9ah,10h,11h-cyclopenta[a]phenanthren-1-yl]-2-methylhept-2-enoic acid

Description

(24E)-3,4-hydroxycucurbita-5,24-diene-26-oic acid belongs to the class of organic compounds known as cucurbitacins. These are polycyclic compounds containing the tetracyclic cucurbitane nucleus skeleton, 19-(10->9b)-abeo-10alanost-5-ene (also known as 9b-methyl-19-nor lanosta-5-ene), with a variety of oxygenation functionalities at different positions. (2e,6r)-6-[(1r,3as,3br,7s,9as,9br,11ar)-7-hydroxy-3a,6,6,9b,11a-pentamethyl-1h,2h,3h,3bh,4h,7h,8h,9h,9ah,10h,11h-cyclopenta[a]phenanthren-1-yl]-2-methylhept-2-enoic acid is found in Russula lepida. Based on a literature review very few articles have been published on (24E)-3,4-hydroxycucurbita-5,24-diene-26-oic acid.

Structure

MOL 3D MOL SDF PDB SMILES InChI

  Mrv1652309052208182D          

 33 36  0  0  1  0            999 V2000
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M  END

     RDKit          3D

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M  END

  Mrv1652309052208182D          

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   -1.6762   -1.3546    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.0361   -0.6122    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4716    0.2340    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7825   -0.5301    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9779    0.8854    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  1  0  0  0
  8  6  1  6  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  1  0  0  0
 11 13  1  0  0  0  0
 13 14  1  1  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 17 16  1  6  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  6  0  0  0
 20 22  1  0  0  0  0
 16 22  1  0  0  0  0
 22 23  1  0  0  0  0
 22 24  1  0  0  0  0
 17 25  1  0  0  0  0
 13 25  1  0  0  0  0
 25 26  1  6  0  0  0
 25 27  1  0  0  0  0
 27 28  1  0  0  0  0
 28 29  1  0  0  0  0
  8 29  1  0  0  0  0
 11 29  1  0  0  0  0
 29 30  1  6  0  0  0
  2 31  1  0  0  0  0
 31 32  2  0  0  0  0
 31 33  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0209052

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@H](CC\C=C(/C)C(O)=O)[C@H]1CC[C@@]2(C)[C@@H]3CC=C4[C@@H](CC[C@H](O)C4(C)C)[C@]3(C)CC[C@]12C

> <INCHI_IDENTIFIER>
InChI=1S/C30H48O3/c1-19(9-8-10-20(2)26(32)33)21-15-16-30(7)24-13-11-22-23(12-14-25(31)27(22,3)4)28(24,5)17-18-29(21,30)6/h10-11,19,21,23-25,31H,8-9,12-18H2,1-7H3,(H,32,33)/b20-10+/t19-,21-,23-,24-,25+,28+,29-,30+/m1/s1

> <INCHI_KEY>
JMOPTHLWCJXLBX-MTPQQZNSSA-N

> <FORMULA>
C30H48O3

> <MOLECULAR_WEIGHT>
456.711

> <EXACT_MASS>
456.360345406

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
81

> <JCHEM_AVERAGE_POLARIZABILITY>
55.532458899234044

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2E,6R)-6-[(1R,2S,5S,10R,11S,14R,15R)-5-hydroxy-1,6,6,11,15-pentamethyltetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadec-7-en-14-yl]-2-methylhept-2-enoic acid

> <JCHEM_LOGP>
6.942022944666666

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
19.408471039623986

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.772299807517059

> <JCHEM_PKA_STRONGEST_BASIC>
-0.8705357557082835

> <JCHEM_POLAR_SURFACE_AREA>
57.53

> <JCHEM_REFRACTIVITY>
136.52849999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(2E,6R)-6-[(1R,2S,5S,10R,11S,14R,15R)-5-hydroxy-1,6,6,11,15-pentamethyltetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadec-7-en-14-yl]-2-methylhept-2-enoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 05-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   05-SEP-22         0                                  
HETATM    1  C   UNK     0      -9.974   2.074   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0     -10.555   0.648   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -9.610  -0.568   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -8.084  -0.358   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -7.139  -1.573   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -5.613  -1.363   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -5.033   0.064   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -4.668  -2.579   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -5.096  -4.058   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -3.822  -4.922   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -2.606  -3.977   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -2.237  -5.472   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -1.090  -4.248   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -0.567  -5.696   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       0.949  -5.967   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       1.942  -4.790   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       1.419  -3.342   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       2.412  -2.164   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       3.928  -2.436   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       4.451  -3.884   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       5.967  -4.155   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       3.458  -5.061   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       4.600  -6.094   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       3.240  -6.586   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -0.097  -3.071   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       0.896  -1.893   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      -0.620  -1.622   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      -2.136  -1.351   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      -3.129  -2.529   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      -3.801  -1.143   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0     -12.080   0.437   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0     -12.661  -0.990   0.000  0.00  0.00           O+0
HETATM   33  O   UNK     0     -13.025   1.653   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   31                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9   29                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   13   29                                             
CONECT   12   11                                                            
CONECT   13   11   14   25                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17   22                                                  
CONECT   17   16   18   25                                                  
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   16   23   24                                             
CONECT   23   22                                                            
CONECT   24   22                                                            
CONECT   25   17   13   26   27                                             
CONECT   26   25                                                            
CONECT   27   25   28                                                       
CONECT   28   27   29                                                       
CONECT   29   28    8   11   30                                             
CONECT   30   29                                                            
CONECT   31    2   32   33                                                  
CONECT   32   31                                                            
CONECT   33   31                                                            
MASTER        0    0    0    0    0    0    0    0   33    0   72    0
END

View in JSmol

Synonyms

Value	Source
(24E)-3,4-Hydroxycucurbita-5,24-diene-26-Oate	Generator

Chemical Formula

C₃₀H₄₈O₃

Average Mass

456.7110 Da

Monoisotopic Mass

456.36035 Da

IUPAC Name

(2E,6R)-6-[(1R,2S,5S,10R,11S,14R,15R)-5-hydroxy-1,6,6,11,15-pentamethyltetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadec-7-en-14-yl]-2-methylhept-2-enoic acid

Traditional Name

(2E,6R)-6-[(1R,2S,5S,10R,11S,14R,15R)-5-hydroxy-1,6,6,11,15-pentamethyltetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadec-7-en-14-yl]-2-methylhept-2-enoic acid

CAS Registry Number

Not Available

SMILES

C[C@H](CC\C=C(/C)C(O)=O)[C@H]1CC[C@@]2(C)[C@@H]3CC=C4[C@@H](CC[C@H](O)C4(C)C)[C@]3(C)CC[C@]12C

InChI Identifier

InChI=1S/C30H48O3/c1-19(9-8-10-20(2)26(32)33)21-15-16-30(7)24-13-11-22-23(12-14-25(31)27(22,3)4)28(24,5)17-18-29(21,30)6/h10-11,19,21,23-25,31H,8-9,12-18H2,1-7H3,(H,32,33)/b20-10+/t19-,21-,23-,24-,25+,28+,29-,30+/m1/s1

InChI Key

JMOPTHLWCJXLBX-MTPQQZNSSA-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
Russula lepida	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as cucurbitacins. These are polycyclic compounds containing the tetracyclic cucurbitane nucleus skeleton, 19-(10->9b)-abeo-10alanost-5-ene (also known as 9b-methyl-19-nor lanosta-5-ene), with a variety of oxygenation functionalities at different positions.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Steroids and steroid derivatives

Sub Class

Cucurbitacins

Direct Parent

Cucurbitacins

Alternative Parents

Substituents

Cucurbitacin skeleton
Triterpenoid
Steroid acid
Hydroxysteroid
3-hydroxy-delta-5-steroid
3-hydroxysteroid
3-beta-hydroxy-delta-5-steroid
3-beta-hydroxysteroid
14-alpha-methylsteroid
Delta-5-steroid
Medium-chain fatty acid
Hydroxy fatty acid
Methyl-branched fatty acid
Branched fatty acid
Unsaturated fatty acid
Fatty acid
Fatty acyl
Cyclic alcohol
Secondary alcohol
Carboxylic acid derivative
Carboxylic acid
Monocarboxylic acid or derivatives
Organic oxygen compound
Carbonyl group
Hydrocarbon derivative
Organic oxide
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	6.94	ChemAxon
pKa (Strongest Acidic)	4.77	ChemAxon
pKa (Strongest Basic)	-0.87	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	57.53 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	136.53 m³·mol⁻¹	ChemAxon
Polarizability	55.53 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	No	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

78441906

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

15479506

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (2e,6r)-6-[(1r,3as,3br,7s,9as,9br,11ar)-7-hydroxy-3a,6,6,9b,11a-pentamethyl-1h,2h,3h,3bh,4h,7h,8h,9h,9ah,10h,11h-cyclopenta[a]phenanthren-1-yl]-2-methylhept-2-enoic acid (NP0209052)

MOL for NP0209052 ((2e,6r)-6-[(1r,3as,3br,7s,9as,9br,11ar)-7-hydroxy-3a,6,6,9b,11a-pentamethyl-1h,2h,3h,3bh,4h,7h,8h,9h,9ah,10h,11h-cyclopenta[a]phenanthren-1-yl]-2-methylhept-2-enoic acid)

3D MOL for NP0209052 ((2e,6r)-6-[(1r,3as,3br,7s,9as,9br,11ar)-7-hydroxy-3a,6,6,9b,11a-pentamethyl-1h,2h,3h,3bh,4h,7h,8h,9h,9ah,10h,11h-cyclopenta[a]phenanthren-1-yl]-2-methylhept-2-enoic acid)

3D SDF for NP0209052 ((2e,6r)-6-[(1r,3as,3br,7s,9as,9br,11ar)-7-hydroxy-3a,6,6,9b,11a-pentamethyl-1h,2h,3h,3bh,4h,7h,8h,9h,9ah,10h,11h-cyclopenta[a]phenanthren-1-yl]-2-methylhept-2-enoic acid)

3D-SDF for NP0209052 ((2e,6r)-6-[(1r,3as,3br,7s,9as,9br,11ar)-7-hydroxy-3a,6,6,9b,11a-pentamethyl-1h,2h,3h,3bh,4h,7h,8h,9h,9ah,10h,11h-cyclopenta[a]phenanthren-1-yl]-2-methylhept-2-enoic acid)

PDB for NP0209052 ((2e,6r)-6-[(1r,3as,3br,7s,9as,9br,11ar)-7-hydroxy-3a,6,6,9b,11a-pentamethyl-1h,2h,3h,3bh,4h,7h,8h,9h,9ah,10h,11h-cyclopenta[a]phenanthren-1-yl]-2-methylhept-2-enoic acid)

3D PDB for NP0209052 ((2e,6r)-6-[(1r,3as,3br,7s,9as,9br,11ar)-7-hydroxy-3a,6,6,9b,11a-pentamethyl-1h,2h,3h,3bh,4h,7h,8h,9h,9ah,10h,11h-cyclopenta[a]phenanthren-1-yl]-2-methylhept-2-enoic acid)

SMILES for NP0209052 ((2e,6r)-6-[(1r,3as,3br,7s,9as,9br,11ar)-7-hydroxy-3a,6,6,9b,11a-pentamethyl-1h,2h,3h,3bh,4h,7h,8h,9h,9ah,10h,11h-cyclopenta[a]phenanthren-1-yl]-2-methylhept-2-enoic acid)

INCHI for NP0209052 ((2e,6r)-6-[(1r,3as,3br,7s,9as,9br,11ar)-7-hydroxy-3a,6,6,9b,11a-pentamethyl-1h,2h,3h,3bh,4h,7h,8h,9h,9ah,10h,11h-cyclopenta[a]phenanthren-1-yl]-2-methylhept-2-enoic acid)

Structure for NP0209052 ((2e,6r)-6-[(1r,3as,3br,7s,9as,9br,11ar)-7-hydroxy-3a,6,6,9b,11a-pentamethyl-1h,2h,3h,3bh,4h,7h,8h,9h,9ah,10h,11h-cyclopenta[a]phenanthren-1-yl]-2-methylhept-2-enoic acid)

3D Structure for NP0209052 ((2e,6r)-6-[(1r,3as,3br,7s,9as,9br,11ar)-7-hydroxy-3a,6,6,9b,11a-pentamethyl-1h,2h,3h,3bh,4h,7h,8h,9h,9ah,10h,11h-cyclopenta[a]phenanthren-1-yl]-2-methylhept-2-enoic acid)