NP-MRD: Showing NP-Card for (2s,3r,4r,5r)-2-[(1r,3as,3br,5as,7s,8r,9as,9bs,11as)-7,8-dihydroxy-9a,11a-dimethyl-tetradecahydro-1h-cyclopenta[a]phenanthren-1-yl]-5,6-dimethylheptane-3,4-diol (NP0273451)

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Record Information

Version

2.0

Created at

2022-09-08 20:29:32 UTC

Updated at

2022-09-08 20:29:32 UTC

NP-MRD ID

NP0273451

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2s,3r,4r,5r)-2-[(1r,3as,3br,5as,7s,8r,9as,9bs,11as)-7,8-dihydroxy-9a,11a-dimethyl-tetradecahydro-1h-cyclopenta[a]phenanthren-1-yl]-5,6-dimethylheptane-3,4-diol

Description

6-Deoxo-24-epicastasterone belongs to the class of organic compounds known as tetrahydroxy bile acids, alcohols and derivatives. These are prenol lipids structurally characterized by a bile acid or alcohol which bears four hydroxyl groups. (2s,3r,4r,5r)-2-[(1r,3as,3br,5as,7s,8r,9as,9bs,11as)-7,8-dihydroxy-9a,11a-dimethyl-tetradecahydro-1h-cyclopenta[a]phenanthren-1-yl]-5,6-dimethylheptane-3,4-diol is found in Viscaria vulgaris and Ornithopus sativus. (2s,3r,4r,5r)-2-[(1r,3as,3br,5as,7s,8r,9as,9bs,11as)-7,8-dihydroxy-9a,11a-dimethyl-tetradecahydro-1h-cyclopenta[a]phenanthren-1-yl]-5,6-dimethylheptane-3,4-diol was first documented in 2010 (PMID: 20973008). Based on a literature review a small amount of articles have been published on 6-Deoxo-24-epicastasterone (PMID: 25092597) (PMID: 23702098).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309082222292D          

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M  END

     RDKit          3D

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M  END


  Mrv1652309082222292D          

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   13.0984   -3.3803    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.2914   -3.2088    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.0365   -2.4242    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   11.4234   -2.9762    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  1  0  0  0
  4  6  1  0  0  0  0
  6  7  1  6  0  0  0
  6  8  1  0  0  0  0
  8  9  1  6  0  0  0
  8 10  1  0  0  0  0
 10 11  1  6  0  0  0
 12 10  1  1  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 15 14  1  1  0  0  0
 15 16  1  0  0  0  0
 16 17  1  6  0  0  0
 17 18  1  0  0  0  0
 19 18  1  1  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  6  0  0  0
 21 23  1  0  0  0  0
 23 24  1  6  0  0  0
 23 25  1  0  0  0  0
 25 26  1  0  0  0  0
 19 26  1  0  0  0  0
 26 27  1  1  0  0  0
 26 28  1  0  0  0  0
 16 28  1  0  0  0  0
 28 29  1  1  0  0  0
 29 30  1  0  0  0  0
 30 31  1  0  0  0  0
 15 31  1  0  0  0  0
 12 31  1  0  0  0  0
 31 32  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0273451

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)[C@@H](C)[C@@H](O)[C@H](O)[C@@H](C)[C@H]1CC[C@H]2[C@@H]3CC[C@H]4C[C@H](O)[C@H](O)C[C@]4(C)[C@H]3CC[C@]12C

> <INCHI_IDENTIFIER>
InChI=1S/C28H50O4/c1-15(2)16(3)25(31)26(32)17(4)20-9-10-21-19-8-7-18-13-23(29)24(30)14-28(18,6)22(19)11-12-27(20,21)5/h15-26,29-32H,7-14H2,1-6H3/t16-,17+,18+,19+,20-,21+,22+,23+,24-,25-,26-,27-,28+/m1/s1

> <INCHI_KEY>
VXBLCLVRWCLEOX-DGBFLIRNSA-N

> <FORMULA>
C28H50O4

> <MOLECULAR_WEIGHT>
450.704

> <EXACT_MASS>
450.37091009

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
82

> <JCHEM_AVERAGE_POLARIZABILITY>
54.79461198364229

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1S,2S,4R,5S,7S,10R,11S,14R,15S)-14-[(2S,3R,4R,5R)-3,4-dihydroxy-5,6-dimethylheptan-2-yl]-2,15-dimethyltetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadecane-4,5-diol

> <JCHEM_LOGP>
4.424869327333334

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.056499775141976

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.457880230015501

> <JCHEM_PKA_STRONGEST_BASIC>
-3.148853305169803

> <JCHEM_POLAR_SURFACE_AREA>
80.92

> <JCHEM_REFRACTIVITY>
128.5536

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1S,2S,4R,5S,7S,10R,11S,14R,15S)-14-[(2S,3R,4R,5R)-3,4-dihydroxy-5,6-dimethylheptan-2-yl]-2,15-dimethyltetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadecane-4,5-diol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 08-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   08-SEP-22         0                                  
HETATM    1  C   UNK     0      13.059  -3.899   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      14.393  -4.669   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      14.393  -6.209   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      15.726  -3.899   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      15.726  -2.359   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      17.060  -4.669   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      17.060  -6.209   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      18.394  -3.899   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      18.394  -2.359   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      19.728  -4.669   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      19.728  -6.209   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      21.061  -3.899   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      21.222  -2.367   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      22.729  -2.047   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      23.499  -3.381   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      25.005  -3.701   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      26.035  -2.556   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      27.542  -2.877   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      28.018  -4.341   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      29.524  -4.661   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      30.000  -6.126   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      31.506  -6.446   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0      28.969  -7.271   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0      29.445  -8.735   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0      27.463  -6.950   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      26.987  -5.486   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      25.957  -6.630   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      25.481  -5.166   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      24.450  -6.310   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      22.944  -5.990   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      22.468  -4.525   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      21.324  -5.556   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13   31                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16   31                                                  
CONECT   16   15   17   28                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20   26                                                  
CONECT   20   19   21                                                       
CONECT   21   20   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23   26                                                       
CONECT   26   25   19   27   28                                             
CONECT   27   26                                                            
CONECT   28   26   16   29                                                  
CONECT   29   28   30                                                       
CONECT   30   29   31                                                       
CONECT   31   30   15   12   32                                             
CONECT   32   31                                                            
MASTER        0    0    0    0    0    0    0    0   32    0   70    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₈H₅₀O₄

Average Mass

450.7040 Da

Monoisotopic Mass

450.37091 Da

IUPAC Name

(1S,2S,4R,5S,7S,10R,11S,14R,15S)-14-[(2S,3R,4R,5R)-3,4-dihydroxy-5,6-dimethylheptan-2-yl]-2,15-dimethyltetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadecane-4,5-diol

Traditional Name

(1S,2S,4R,5S,7S,10R,11S,14R,15S)-14-[(2S,3R,4R,5R)-3,4-dihydroxy-5,6-dimethylheptan-2-yl]-2,15-dimethyltetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadecane-4,5-diol

CAS Registry Number

Not Available

SMILES

CC(C)[C@@H](C)[C@@H](O)[C@H](O)[C@@H](C)[C@H]1CC[C@H]2[C@@H]3CC[C@H]4C[C@H](O)[C@H](O)C[C@]4(C)[C@H]3CC[C@]12C

InChI Identifier

InChI=1S/C28H50O4/c1-15(2)16(3)25(31)26(32)17(4)20-9-10-21-19-8-7-18-13-23(29)24(30)14-28(18,6)22(19)11-12-27(20,21)5/h15-26,29-32H,7-14H2,1-6H3/t16-,17+,18+,19+,20-,21+,22+,23+,24-,25-,26-,27-,28+/m1/s1

InChI Key

VXBLCLVRWCLEOX-DGBFLIRNSA-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
Lychnis viscaria	LOTUS Database	35616633
Ornithopus sativus	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as tetrahydroxy bile acids, alcohols and derivatives. These are prenol lipids structurally characterized by a bile acid or alcohol which bears four hydroxyl 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

Tetrahydroxy bile acids, alcohols and derivatives

Alternative Parents

Substituents

Ergosterol-skeleton
Ergostane-skeleton
Tetrahydroxy bile acid, alcohol, or derivatives
23-hydroxysteroid
22-hydroxysteroid
3-hydroxysteroid
2-hydroxysteroid
3-alpha-hydroxysteroid
Hydroxysteroid
Cyclic alcohol
Secondary alcohol
Alcohol
Hydrocarbon derivative
Organic oxygen compound
Organooxygen compound
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	4.42	ChemAxon
pKa (Strongest Acidic)	13.46	ChemAxon
pKa (Strongest Basic)	-3.1	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	80.92 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	128.55 m³·mol⁻¹	ChemAxon
Polarizability	54.79 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	No	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00036612

Chemspider ID

57620762

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

101682289

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Wang L, Duan C, Wu D, Guan Y: Quantification of endogenous brassinosteroids in sub-gram plant tissues by in-line matrix solid-phase dispersion-tandem solid phase extraction coupled with high performance liquid chromatography-tandem mass spectrometry. J Chromatogr A. 2014 Sep 12;1359:44-51. doi: 10.1016/j.chroma.2014.07.037. Epub 2014 Jul 23. [PubMed:25092597 ]
Wu Q, Wu D, Shen Z, Duan C, Guan Y: Quantification of endogenous brassinosteroids in plant by on-line two-dimensional microscale solid phase extraction-on column derivatization coupled with high performance liquid chromatography-tandem mass spectrometry. J Chromatogr A. 2013 Jul 5;1297:56-63. doi: 10.1016/j.chroma.2013.04.043. Epub 2013 Apr 22. [PubMed:23702098 ]
Huo F, Bai Y, Liu H: Fragmentation investigation of brassinosteroid compounds by ion trap and quadrupole time-of-flight mass spectrometry. Rapid Commun Mass Spectrom. 2010 Nov 30;24(22):3325-34. doi: 10.1002/rcm.4772. [PubMed:20973008 ]
LOTUS database [Link]

Showing NP-Card for (2s,3r,4r,5r)-2-[(1r,3as,3br,5as,7s,8r,9as,9bs,11as)-7,8-dihydroxy-9a,11a-dimethyl-tetradecahydro-1h-cyclopenta[a]phenanthren-1-yl]-5,6-dimethylheptane-3,4-diol (NP0273451)

MOL for NP0273451 ((2s,3r,4r,5r)-2-[(1r,3as,3br,5as,7s,8r,9as,9bs,11as)-7,8-dihydroxy-9a,11a-dimethyl-tetradecahydro-1h-cyclopenta[a]phenanthren-1-yl]-5,6-dimethylheptane-3,4-diol)

3D MOL for NP0273451 ((2s,3r,4r,5r)-2-[(1r,3as,3br,5as,7s,8r,9as,9bs,11as)-7,8-dihydroxy-9a,11a-dimethyl-tetradecahydro-1h-cyclopenta[a]phenanthren-1-yl]-5,6-dimethylheptane-3,4-diol)

3D SDF for NP0273451 ((2s,3r,4r,5r)-2-[(1r,3as,3br,5as,7s,8r,9as,9bs,11as)-7,8-dihydroxy-9a,11a-dimethyl-tetradecahydro-1h-cyclopenta[a]phenanthren-1-yl]-5,6-dimethylheptane-3,4-diol)

3D-SDF for NP0273451 ((2s,3r,4r,5r)-2-[(1r,3as,3br,5as,7s,8r,9as,9bs,11as)-7,8-dihydroxy-9a,11a-dimethyl-tetradecahydro-1h-cyclopenta[a]phenanthren-1-yl]-5,6-dimethylheptane-3,4-diol)

PDB for NP0273451 ((2s,3r,4r,5r)-2-[(1r,3as,3br,5as,7s,8r,9as,9bs,11as)-7,8-dihydroxy-9a,11a-dimethyl-tetradecahydro-1h-cyclopenta[a]phenanthren-1-yl]-5,6-dimethylheptane-3,4-diol)

3D PDB for NP0273451 ((2s,3r,4r,5r)-2-[(1r,3as,3br,5as,7s,8r,9as,9bs,11as)-7,8-dihydroxy-9a,11a-dimethyl-tetradecahydro-1h-cyclopenta[a]phenanthren-1-yl]-5,6-dimethylheptane-3,4-diol)

SMILES for NP0273451 ((2s,3r,4r,5r)-2-[(1r,3as,3br,5as,7s,8r,9as,9bs,11as)-7,8-dihydroxy-9a,11a-dimethyl-tetradecahydro-1h-cyclopenta[a]phenanthren-1-yl]-5,6-dimethylheptane-3,4-diol)

INCHI for NP0273451 ((2s,3r,4r,5r)-2-[(1r,3as,3br,5as,7s,8r,9as,9bs,11as)-7,8-dihydroxy-9a,11a-dimethyl-tetradecahydro-1h-cyclopenta[a]phenanthren-1-yl]-5,6-dimethylheptane-3,4-diol)

Structure for NP0273451 ((2s,3r,4r,5r)-2-[(1r,3as,3br,5as,7s,8r,9as,9bs,11as)-7,8-dihydroxy-9a,11a-dimethyl-tetradecahydro-1h-cyclopenta[a]phenanthren-1-yl]-5,6-dimethylheptane-3,4-diol)

3D Structure for NP0273451 ((2s,3r,4r,5r)-2-[(1r,3as,3br,5as,7s,8r,9as,9bs,11as)-7,8-dihydroxy-9a,11a-dimethyl-tetradecahydro-1h-cyclopenta[a]phenanthren-1-yl]-5,6-dimethylheptane-3,4-diol)