NP-MRD: Showing NP-Card for (1s,2r,5r,6r,9r,10r,13s,15s)-6,10-dimethyl-5-[(2r)-6-methyl-5-methylideneheptan-2-yl]-16,17-dioxapentacyclo[13.2.2.0¹,⁹.0²,⁶.0¹⁰,¹⁵]nonadec-18-en-13-ol (NP0256077)

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Record Information

Version

1.0

Created at

2022-09-07 20:47:35 UTC

Updated at

2022-09-07 20:47:35 UTC

NP-MRD ID

NP0256077

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1s,2r,5r,6r,9r,10r,13s,15s)-6,10-dimethyl-5-[(2r)-6-methyl-5-methylideneheptan-2-yl]-16,17-dioxapentacyclo[13.2.2.0¹,⁹.0²,⁶.0¹⁰,¹⁵]nonadec-18-en-13-ol

Description

5Alpha,8alpha-Epidioxyergosta-6,24(28)-diene-3beta-ol belongs to the class of organic compounds known as ergostane steroids. These are steroids with a structure based on the ergostane skeleton, which arises from the methylation of cholestane at the 24-position. Thus, 5alpha,8alpha-epidioxyergosta-6,24(28)-diene-3beta-ol is considered to be a sterol. (1s,2r,5r,6r,9r,10r,13s,15s)-6,10-dimethyl-5-[(2r)-6-methyl-5-methylideneheptan-2-yl]-16,17-dioxapentacyclo[13.2.2.0¹,⁹.0²,⁶.0¹⁰,¹⁵]nonadec-18-en-13-ol is found in Eunicella cavolini, Metridium senile, Sinularia flexibilis and Svenzea zeai. Based on a literature review very few articles have been published on 5alpha,8alpha-Epidioxyergosta-6,24(28)-diene-3beta-ol.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309072222472D          

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M  END

     RDKit          3D

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M  END


  Mrv1652309072222472D          

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 27 28  1  0  0  0  0
 11 28  1  6  0  0  0
  2 29  1  0  0  0  0
 29 30  1  0  0  0  0
 29 31  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0256077

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)C(=C)CC[C@@H](C)[C@H]1CC[C@@H]2[C@]1(C)CC[C@@H]1[C@@]3(C)CC[C@H](O)C[C@@]33OO[C@@]21C=C3

> <INCHI_IDENTIFIER>
InChI=1S/C28H44O3/c1-18(2)19(3)7-8-20(4)22-9-10-23-25(22,5)13-12-24-26(6)14-11-21(29)17-27(26)15-16-28(23,24)31-30-27/h15-16,18,20-24,29H,3,7-14,17H2,1-2,4-6H3/t20-,21+,22-,23-,24-,25-,26-,27-,28+/m1/s1

> <INCHI_KEY>
XGUKSASAYIQRBB-WBIZBJRUSA-N

> <FORMULA>
C28H44O3

> <MOLECULAR_WEIGHT>
428.657

> <EXACT_MASS>
428.329045277

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
75

> <JCHEM_AVERAGE_POLARIZABILITY>
52.28439204645312

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1S,2R,5R,6R,9R,10R,13S,15S)-6,10-dimethyl-5-[(2R)-6-methyl-5-methylideneheptan-2-yl]-16,17-dioxapentacyclo[13.2.2.0^{1,9}.0^{2,6}.0^{10,15}]nonadec-18-en-13-ol

> <JCHEM_LOGP>
6.362214693333334

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
15.1490254826832

> <JCHEM_PKA_STRONGEST_BASIC>
-2.7336162538743682

> <JCHEM_POLAR_SURFACE_AREA>
38.69

> <JCHEM_REFRACTIVITY>
125.48499999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(1S,2R,5R,6R,9R,10R,13S,15S)-6,10-dimethyl-5-[(2R)-6-methyl-5-methylideneheptan-2-yl]-16,17-dioxapentacyclo[13.2.2.0^{1,9}.0^{2,6}.0^{10,15}]nonadec-18-en-13-ol

> <JCHEM_VEBER_RULE>
1

$$$$

HEADER    PROTEIN                                 07-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   07-SEP-22         0                                  
HETATM    1  C   UNK     0      18.777   5.166   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      18.123   3.771   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      16.589   3.641   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      15.708   4.904   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      14.174   4.773   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      13.293   6.037   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      13.520   3.379   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      14.263   2.031   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      13.210   0.907   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      11.816   1.561   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      10.202   1.554   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       9.276   0.045   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       7.542  -0.194   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       6.243   1.009   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       4.687   0.579   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       4.082   2.017   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       2.542   1.999   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       4.659   3.487   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       6.191   3.639   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       7.214   2.429   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       8.389   1.433   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       8.882   2.658   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       9.540   4.100   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      11.056   4.368   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      12.007   3.089   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      12.565   4.524   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0       7.556   0.988   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0       8.943   1.179   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0      19.003   2.508   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      20.538   2.639   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      18.349   1.114   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   29                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8   25                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11   25                                                  
CONECT   11   10   12   22   28                                             
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15   20   27                                             
CONECT   15   14   16                                                       
CONECT   16   15   17   18                                                  
CONECT   17   16                                                            
CONECT   18   16   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   14   21   22                                             
CONECT   21   20                                                            
CONECT   22   20   11   23                                                  
CONECT   23   22   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24    7   10   26                                             
CONECT   26   25                                                            
CONECT   27   14   28                                                       
CONECT   28   27   11                                                       
CONECT   29    2   30   31                                                  
CONECT   30   29                                                            
CONECT   31   29                                                            
MASTER        0    0    0    0    0    0    0    0   31    0   70    0
END

View in JSmol

Synonyms

Value	Source
5a,8a-Epidioxyergosta-6,24(28)-diene-3b-ol	Generator
5Α,8α-epidioxyergosta-6,24(28)-diene-3β-ol	Generator

Chemical Formula

C₂₈H₄₄O₃

Average Mass

428.6570 Da

Monoisotopic Mass

428.32905 Da

IUPAC Name

(1S,2R,5R,6R,9R,10R,13S,15S)-6,10-dimethyl-5-[(2R)-6-methyl-5-methylideneheptan-2-yl]-16,17-dioxapentacyclo[13.2.2.0^{1,9}.0^{2,6}.0^{10,15}]nonadec-18-en-13-ol

Traditional Name

(1S,2R,5R,6R,9R,10R,13S,15S)-6,10-dimethyl-5-[(2R)-6-methyl-5-methylideneheptan-2-yl]-16,17-dioxapentacyclo[13.2.2.0^{1,9}.0^{2,6}.0^{10,15}]nonadec-18-en-13-ol

CAS Registry Number

Not Available

SMILES

CC(C)C(=C)CC[C@@H](C)[C@H]1CC[C@@H]2[C@]1(C)CC[C@@H]1[C@@]3(C)CC[C@H](O)C[C@@]33OO[C@@]21C=C3

InChI Identifier

InChI=1S/C28H44O3/c1-18(2)19(3)7-8-20(4)22-9-10-23-25(22,5)13-12-24-26(6)14-11-21(29)17-27(26)15-16-28(23,24)31-30-27/h15-16,18,20-24,29H,3,7-14,17H2,1-2,4-6H3/t20-,21+,22-,23-,24-,25-,26-,27-,28+/m1/s1

InChI Key

XGUKSASAYIQRBB-WBIZBJRUSA-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
Eunicella cavolini	LOTUS Database	35616633
Metridium senile	LOTUS Database	35616633
Sinularia flexibilis	LOTUS Database	35616633
Svenzea zeai	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as ergostane steroids. These are steroids with a structure based on the ergostane skeleton, which arises from the methylation of cholestane at the 24-position.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Steroids and steroid derivatives

Sub Class

Ergostane steroids

Direct Parent

Ergostane steroids

Alternative Parents

Substituents

Ergostane-skeleton
Ortho-dioxane
Cyclic alcohol
Dialkyl peroxide
Secondary alcohol
Oxacycle
Organoheterocyclic compound
Organic oxygen compound
Hydrocarbon derivative
Organooxygen compound
Alcohol
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic 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	6.36	ChemAxon
pKa (Strongest Acidic)	15.15	ChemAxon
pKa (Strongest Basic)	-2.7	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	38.69 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	125.48 m³·mol⁻¹	ChemAxon
Polarizability	52.28 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	Yes	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

29212489

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

14394130

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (1s,2r,5r,6r,9r,10r,13s,15s)-6,10-dimethyl-5-[(2r)-6-methyl-5-methylideneheptan-2-yl]-16,17-dioxapentacyclo[13.2.2.0¹,⁹.0²,⁶.0¹⁰,¹⁵]nonadec-18-en-13-ol (NP0256077)

MOL for NP0256077 ((1s,2r,5r,6r,9r,10r,13s,15s)-6,10-dimethyl-5-[(2r)-6-methyl-5-methylideneheptan-2-yl]-16,17-dioxapentacyclo[13.2.2.0¹,⁹.0²,⁶.0¹⁰,¹⁵]nonadec-18-en-13-ol)

3D MOL for NP0256077 ((1s,2r,5r,6r,9r,10r,13s,15s)-6,10-dimethyl-5-[(2r)-6-methyl-5-methylideneheptan-2-yl]-16,17-dioxapentacyclo[13.2.2.0¹,⁹.0²,⁶.0¹⁰,¹⁵]nonadec-18-en-13-ol)

3D SDF for NP0256077 ((1s,2r,5r,6r,9r,10r,13s,15s)-6,10-dimethyl-5-[(2r)-6-methyl-5-methylideneheptan-2-yl]-16,17-dioxapentacyclo[13.2.2.0¹,⁹.0²,⁶.0¹⁰,¹⁵]nonadec-18-en-13-ol)

3D-SDF for NP0256077 ((1s,2r,5r,6r,9r,10r,13s,15s)-6,10-dimethyl-5-[(2r)-6-methyl-5-methylideneheptan-2-yl]-16,17-dioxapentacyclo[13.2.2.0¹,⁹.0²,⁶.0¹⁰,¹⁵]nonadec-18-en-13-ol)

PDB for NP0256077 ((1s,2r,5r,6r,9r,10r,13s,15s)-6,10-dimethyl-5-[(2r)-6-methyl-5-methylideneheptan-2-yl]-16,17-dioxapentacyclo[13.2.2.0¹,⁹.0²,⁶.0¹⁰,¹⁵]nonadec-18-en-13-ol)

3D PDB for NP0256077 ((1s,2r,5r,6r,9r,10r,13s,15s)-6,10-dimethyl-5-[(2r)-6-methyl-5-methylideneheptan-2-yl]-16,17-dioxapentacyclo[13.2.2.0¹,⁹.0²,⁶.0¹⁰,¹⁵]nonadec-18-en-13-ol)

SMILES for NP0256077 ((1s,2r,5r,6r,9r,10r,13s,15s)-6,10-dimethyl-5-[(2r)-6-methyl-5-methylideneheptan-2-yl]-16,17-dioxapentacyclo[13.2.2.0¹,⁹.0²,⁶.0¹⁰,¹⁵]nonadec-18-en-13-ol)

INCHI for NP0256077 ((1s,2r,5r,6r,9r,10r,13s,15s)-6,10-dimethyl-5-[(2r)-6-methyl-5-methylideneheptan-2-yl]-16,17-dioxapentacyclo[13.2.2.0¹,⁹.0²,⁶.0¹⁰,¹⁵]nonadec-18-en-13-ol)

Structure for NP0256077 ((1s,2r,5r,6r,9r,10r,13s,15s)-6,10-dimethyl-5-[(2r)-6-methyl-5-methylideneheptan-2-yl]-16,17-dioxapentacyclo[13.2.2.0¹,⁹.0²,⁶.0¹⁰,¹⁵]nonadec-18-en-13-ol)

3D Structure for NP0256077 ((1s,2r,5r,6r,9r,10r,13s,15s)-6,10-dimethyl-5-[(2r)-6-methyl-5-methylideneheptan-2-yl]-16,17-dioxapentacyclo[13.2.2.0¹,⁹.0²,⁶.0¹⁰,¹⁵]nonadec-18-en-13-ol)