NP-MRD: Showing NP-Card for (1s,2r,5r,6r,9r,10r,13s,15s)-6,10-dimethyl-5-[(2r,3e)-4-[(1r,2s)-2-methylcyclopropyl]but-3-en-2-yl]-16,17-dioxapentacyclo[13.2.2.0¹,⁹.0²,⁶.0¹⁰,¹⁵]nonadec-18-en-13-ol (NP0325770)

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Record Information

Version

2.0

Created at

2022-09-12 06:46:37 UTC

Updated at

2022-09-12 06:46:38 UTC

NP-MRD ID

NP0325770

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1s,2r,5r,6r,9r,10r,13s,15s)-6,10-dimethyl-5-[(2r,3e)-4-[(1r,2s)-2-methylcyclopropyl]but-3-en-2-yl]-16,17-dioxapentacyclo[13.2.2.0¹,⁹.0²,⁶.0¹⁰,¹⁵]nonadec-18-en-13-ol

Description

(1S,2R,5R,6R,9R,10R,13S,15S)-6,10-dimethyl-5-[(2R,3E)-4-[(1R,2S)-2-methylcyclopropyl]but-3-en-2-yl]-16,17-dioxapentacyclo[13.2.2.0¹,⁹.0²,⁶.0¹⁰,¹⁵]Nonadec-18-en-13-ol belongs to the class of organic compounds known as steroids and steroid derivatives. Steroids and steroid derivatives are compounds based on the cyclopenta[a]phenanthrene carbon skeleton, partially or completely hydrogenated; there are usually methyl groups at C-10 and C-13, and often an alkyl group at C-17. By extension, one or more bond scissions, ring expansions and/or ring contractions of the skeleton may have occurred. (1s,2r,5r,6r,9r,10r,13s,15s)-6,10-dimethyl-5-[(2r,3e)-4-[(1r,2s)-2-methylcyclopropyl]but-3-en-2-yl]-16,17-dioxapentacyclo[13.2.2.0¹,⁹.0²,⁶.0¹⁰,¹⁵]nonadec-18-en-13-ol is found in Eunicella cavolini. Based on a literature review very few articles have been published on (1S,2R,5R,6R,9R,10R,13S,15S)-6,10-dimethyl-5-[(2R,3E)-4-[(1R,2S)-2-methylcyclopropyl]but-3-en-2-yl]-16,17-dioxapentacyclo[13.2.2.0¹,⁹.0²,⁶.0¹⁰,¹⁵]Nonadec-18-en-13-ol.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309122208462D          

 30 35  0  0  1  0            999 V2000
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M  END

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M  END


  Mrv1652309122208462D          

 30 35  0  0  1  0            999 V2000
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M  END
> <DATABASE_ID>
NP0325770

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@H](\C=C\[C@@H]1C[C@@H]1C)[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/C27H40O3/c1-17(5-6-19-15-18(19)2)21-7-8-22-24(21,3)11-10-23-25(4)12-9-20(28)16-26(25)13-14-27(22,23)30-29-26/h5-6,13-14,17-23,28H,7-12,15-16H2,1-4H3/b6-5+/t17-,18+,19-,20+,21-,22-,23-,24-,25-,26-,27+/m1/s1

> <INCHI_KEY>
ACIGRLRKXLVDFE-RMVUWKEWSA-N

> <FORMULA>
C27H40O3

> <MOLECULAR_WEIGHT>
412.614

> <EXACT_MASS>
412.297745148

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
70

> <JCHEM_AVERAGE_POLARIZABILITY>
49.440641811601566

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1S,2R,5R,6R,9R,10R,13S,15S)-6,10-dimethyl-5-[(2R,3E)-4-[(1R,2S)-2-methylcyclopropyl]but-3-en-2-yl]-16,17-dioxapentacyclo[13.2.2.0^{1,9}.0^{2,6}.0^{10,15}]nonadec-18-en-13-ol

> <JCHEM_LOGP>
5.4396442799999996

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
15.1490254826832

> <JCHEM_PKA_STRONGEST_BASIC>
-2.7336162538743682

> <JCHEM_POLAR_SURFACE_AREA>
38.69

> <JCHEM_REFRACTIVITY>
120.4209

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(1S,2R,5R,6R,9R,10R,13S,15S)-6,10-dimethyl-5-[(2R,3E)-4-[(1R,2S)-2-methylcyclopropyl]but-3-en-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                                 12-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   12-SEP-22         0                                  
HETATM    1  C   UNK     0      20.040   6.046   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      19.386   4.652   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      19.517   3.117   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      18.123   3.771   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      16.589   3.641   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      15.708   4.904   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      14.174   4.773   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      13.293   6.037   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      13.520   3.379   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      14.263   2.031   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      13.210   0.907   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      11.816   1.561   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      10.202   1.554   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       9.276   0.045   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       7.542  -0.194   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       6.243   1.009   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       4.687   0.579   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       4.082   2.017   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       2.542   1.999   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       4.659   3.487   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       6.191   3.639   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       7.214   2.429   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       8.389   1.433   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       8.882   2.658   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       9.540   4.100   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      11.056   4.368   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      12.007   3.089   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      12.565   4.524   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0       7.556   0.988   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0       8.943   1.179   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2    4                                                       
CONECT    4    3    2    5                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10   27                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13   27                                                  
CONECT   13   12   14   24   30                                             
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17   22   29                                             
CONECT   17   16   18                                                       
CONECT   18   17   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   16   23   24                                             
CONECT   23   22                                                            
CONECT   24   22   13   25                                                  
CONECT   25   24   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26    9   12   28                                             
CONECT   28   27                                                            
CONECT   29   16   30                                                       
CONECT   30   29   13                                                       
MASTER        0    0    0    0    0    0    0    0   30    0   70    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₇H₄₀O₃

Average Mass

412.6140 Da

Monoisotopic Mass

412.29775 Da

IUPAC Name

(1S,2R,5R,6R,9R,10R,13S,15S)-6,10-dimethyl-5-[(2R,3E)-4-[(1R,2S)-2-methylcyclopropyl]but-3-en-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,3E)-4-[(1R,2S)-2-methylcyclopropyl]but-3-en-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

C[C@H](\C=C\[C@@H]1C[C@@H]1C)[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/C27H40O3/c1-17(5-6-19-15-18(19)2)21-7-8-22-24(21,3)11-10-23-25(4)12-9-20(28)16-26(25)13-14-27(22,23)30-29-26/h5-6,13-14,17-23,28H,7-12,15-16H2,1-4H3/b6-5+/t17-,18+,19-,20+,21-,22-,23-,24-,25-,26-,27+/m1/s1

InChI Key

ACIGRLRKXLVDFE-RMVUWKEWSA-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

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as steroids and steroid derivatives. Steroids and steroid derivatives are compounds based on the cyclopenta[a]phenanthrene carbon skeleton, partially or completely hydrogenated; there are usually methyl groups at C-10 and C-13, and often an alkyl group at C-17. By extension, one or more bond scissions, ring expansions and/or ring contractions of the skeleton may have occurred.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Steroids and steroid derivatives

Sub Class

Not Available

Direct Parent

Steroids and steroid derivatives

Alternative Parents

Substituents

Cholane-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	5.44	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	3	ChemAxon
Refractivity	120.42 m³·mol⁻¹	ChemAxon
Polarizability	49.44 Å³	ChemAxon
Number of Rings	6	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	Yes	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

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

162900759

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,3e)-4-[(1r,2s)-2-methylcyclopropyl]but-3-en-2-yl]-16,17-dioxapentacyclo[13.2.2.0¹,⁹.0²,⁶.0¹⁰,¹⁵]nonadec-18-en-13-ol (NP0325770)

MOL for NP0325770 ((1s,2r,5r,6r,9r,10r,13s,15s)-6,10-dimethyl-5-[(2r,3e)-4-[(1r,2s)-2-methylcyclopropyl]but-3-en-2-yl]-16,17-dioxapentacyclo[13.2.2.0¹,⁹.0²,⁶.0¹⁰,¹⁵]nonadec-18-en-13-ol)

3D MOL for NP0325770 ((1s,2r,5r,6r,9r,10r,13s,15s)-6,10-dimethyl-5-[(2r,3e)-4-[(1r,2s)-2-methylcyclopropyl]but-3-en-2-yl]-16,17-dioxapentacyclo[13.2.2.0¹,⁹.0²,⁶.0¹⁰,¹⁵]nonadec-18-en-13-ol)

3D SDF for NP0325770 ((1s,2r,5r,6r,9r,10r,13s,15s)-6,10-dimethyl-5-[(2r,3e)-4-[(1r,2s)-2-methylcyclopropyl]but-3-en-2-yl]-16,17-dioxapentacyclo[13.2.2.0¹,⁹.0²,⁶.0¹⁰,¹⁵]nonadec-18-en-13-ol)

3D-SDF for NP0325770 ((1s,2r,5r,6r,9r,10r,13s,15s)-6,10-dimethyl-5-[(2r,3e)-4-[(1r,2s)-2-methylcyclopropyl]but-3-en-2-yl]-16,17-dioxapentacyclo[13.2.2.0¹,⁹.0²,⁶.0¹⁰,¹⁵]nonadec-18-en-13-ol)

PDB for NP0325770 ((1s,2r,5r,6r,9r,10r,13s,15s)-6,10-dimethyl-5-[(2r,3e)-4-[(1r,2s)-2-methylcyclopropyl]but-3-en-2-yl]-16,17-dioxapentacyclo[13.2.2.0¹,⁹.0²,⁶.0¹⁰,¹⁵]nonadec-18-en-13-ol)

3D PDB for NP0325770 ((1s,2r,5r,6r,9r,10r,13s,15s)-6,10-dimethyl-5-[(2r,3e)-4-[(1r,2s)-2-methylcyclopropyl]but-3-en-2-yl]-16,17-dioxapentacyclo[13.2.2.0¹,⁹.0²,⁶.0¹⁰,¹⁵]nonadec-18-en-13-ol)

SMILES for NP0325770 ((1s,2r,5r,6r,9r,10r,13s,15s)-6,10-dimethyl-5-[(2r,3e)-4-[(1r,2s)-2-methylcyclopropyl]but-3-en-2-yl]-16,17-dioxapentacyclo[13.2.2.0¹,⁹.0²,⁶.0¹⁰,¹⁵]nonadec-18-en-13-ol)

INCHI for NP0325770 ((1s,2r,5r,6r,9r,10r,13s,15s)-6,10-dimethyl-5-[(2r,3e)-4-[(1r,2s)-2-methylcyclopropyl]but-3-en-2-yl]-16,17-dioxapentacyclo[13.2.2.0¹,⁹.0²,⁶.0¹⁰,¹⁵]nonadec-18-en-13-ol)

Structure for NP0325770 ((1s,2r,5r,6r,9r,10r,13s,15s)-6,10-dimethyl-5-[(2r,3e)-4-[(1r,2s)-2-methylcyclopropyl]but-3-en-2-yl]-16,17-dioxapentacyclo[13.2.2.0¹,⁹.0²,⁶.0¹⁰,¹⁵]nonadec-18-en-13-ol)

3D Structure for NP0325770 ((1s,2r,5r,6r,9r,10r,13s,15s)-6,10-dimethyl-5-[(2r,3e)-4-[(1r,2s)-2-methylcyclopropyl]but-3-en-2-yl]-16,17-dioxapentacyclo[13.2.2.0¹,⁹.0²,⁶.0¹⁰,¹⁵]nonadec-18-en-13-ol)