NP-MRD: Showing NP-Card for (1s,2r,6s,7r,9r,11s,12s,15r,16s)-15-[(1s)-1-[(2s,4s,5r)-4,5-dimethyl-6-oxooxan-2-yl]ethyl]-6-hydroxy-2,16-dimethyl-8-oxapentacyclo[9.7.0.0²,⁷.0⁷,⁹.0¹²,¹⁶]octadec-4-en-3-one (NP0313596)

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Record Information

Version

2.0

Created at

2022-09-11 11:15:40 UTC

Updated at

2022-09-11 11:15:40 UTC

NP-MRD ID

NP0313596

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1s,2r,6s,7r,9r,11s,12s,15r,16s)-15-[(1s)-1-[(2s,4s,5r)-4,5-dimethyl-6-oxooxan-2-yl]ethyl]-6-hydroxy-2,16-dimethyl-8-oxapentacyclo[9.7.0.0²,⁷.0⁷,⁹.0¹²,¹⁶]octadec-4-en-3-one

Description

(1S,2R,6S,7R,9R,11S,12S,15R,16S)-15-[(1S)-1-[(2S,4S,5R)-4,5-dimethyl-6-oxooxan-2-yl]ethyl]-6-hydroxy-2,16-dimethyl-8-oxapentacyclo[9.7.0.0²,⁷.0⁷,⁹.0¹²,¹⁶]Octadec-4-en-3-one belongs to the class of organic compounds known as withanolides and derivatives. These are c28 steroids structurally characterized by an ergostane skeleton usually functionalized at carbons 1, 22 and 26 to form a lactone ring. (1s,2r,6s,7r,9r,11s,12s,15r,16s)-15-[(1s)-1-[(2s,4s,5r)-4,5-dimethyl-6-oxooxan-2-yl]ethyl]-6-hydroxy-2,16-dimethyl-8-oxapentacyclo[9.7.0.0²,⁷.0⁷,⁹.0¹²,¹⁶]octadec-4-en-3-one is found in Withania somnifera. Based on a literature review very few articles have been published on (1S,2R,6S,7R,9R,11S,12S,15R,16S)-15-[(1S)-1-[(2S,4S,5R)-4,5-dimethyl-6-oxooxan-2-yl]ethyl]-6-hydroxy-2,16-dimethyl-8-oxapentacyclo[9.7.0.0²,⁷.0⁷,⁹.0¹²,¹⁶]Octadec-4-en-3-one.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309112213152D          

 33 38  0  0  1  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652309112213152D          

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 10 11  1  0  0  0  0
 11 12  1  6  0  0  0
 12 13  1  0  0  0  0
 13 14  1  1  0  0  0
 15 14  1  1  0  0  0
 13 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  1  0  0  0
 16 18  1  0  0  0  0
 18 19  2  0  0  0  0
 19 20  1  0  0  0  0
 20 21  2  0  0  0  0
 20 22  1  0  0  0  0
 15 22  1  0  0  0  0
 22 23  1  1  0  0  0
 22 24  1  0  0  0  0
 11 24  1  0  0  0  0
 24 25  1  1  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 10 27  1  0  0  0  0
  7 27  1  0  0  0  0
 27 28  1  1  0  0  0
  4 29  1  0  0  0  0
 29 30  1  0  0  0  0
 30 31  2  0  0  0  0
 30 32  1  0  0  0  0
  2 32  1  0  0  0  0
 32 33  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0313596

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@@H]([C@H]1CC[C@H]2[C@@H]3C[C@H]4O[C@]44[C@@H](O)C=CC(=O)[C@]4(C)[C@H]3CC[C@]12C)[C@@H]1C[C@H](C)[C@@H](C)C(=O)O1

> <INCHI_IDENTIFIER>
InChI=1S/C28H40O5/c1-14-12-21(32-25(31)15(14)2)16(3)18-6-7-19-17-13-24-28(33-24)23(30)9-8-22(29)27(28,5)20(17)10-11-26(18,19)4/h8-9,14-21,23-24,30H,6-7,10-13H2,1-5H3/t14-,15+,16-,17-,18+,19-,20-,21-,23-,24+,26+,27-,28+/m0/s1

> <INCHI_KEY>
RXCZYUYRSCOXSS-NIWYTSODSA-N

> <FORMULA>
C28H40O5

> <MOLECULAR_WEIGHT>
456.623

> <EXACT_MASS>
456.287574388

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
73

> <JCHEM_AVERAGE_POLARIZABILITY>
52.39170743542998

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1S,2R,6S,7R,9R,11S,12S,15R,16S)-15-[(1S)-1-[(2S,4S,5R)-4,5-dimethyl-6-oxooxan-2-yl]ethyl]-6-hydroxy-2,16-dimethyl-8-oxapentacyclo[9.7.0.0^{2,7}.0^{7,9}.0^{12,16}]octadec-4-en-3-one

> <JCHEM_LOGP>
4.822682061666668

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.44390346313407

> <JCHEM_PKA_STRONGEST_BASIC>
-3.473588445945432

> <JCHEM_POLAR_SURFACE_AREA>
76.13

> <JCHEM_REFRACTIVITY>
124.81069999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1S,2R,6S,7R,9R,11S,12S,15R,16S)-15-[(1S)-1-[(2S,4S,5R)-4,5-dimethyl-6-oxooxan-2-yl]ethyl]-6-hydroxy-2,16-dimethyl-8-oxapentacyclo[9.7.0.0^{2,7}.0^{7,9}.0^{12,16}]octadec-4-en-3-one

> <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      11.945  10.615   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      11.000   9.399   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      11.580   7.972   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      10.635   6.757   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      11.216   5.330   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      12.741   5.119   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      10.270   4.114   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      10.698   2.635   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       9.424   1.771   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       8.208   2.716   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       6.692   2.445   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       6.169   0.996   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       4.653   0.725   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       3.137   0.454   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       3.660   1.903   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       2.144   1.632   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       1.621   0.183   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       1.151   2.809   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       1.675   4.257   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       3.191   4.528   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       3.714   5.977   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       4.183   3.351   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       4.707   4.799   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       5.699   3.622   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       6.222   5.071   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       7.738   5.342   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       8.731   4.164   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       9.403   5.550   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0       9.110   6.967   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0       8.529   8.394   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0       7.004   8.604   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0       9.475   9.609   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       8.894  11.036   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   32                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   29                                                  
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8   27                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11   27                                                  
CONECT   11   10   12   24                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14   15                                                  
CONECT   14   13   15                                                       
CONECT   15   14   13   16   22                                             
CONECT   16   15   17   18                                                  
CONECT   17   16                                                            
CONECT   18   16   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   15   23   24                                             
CONECT   23   22                                                            
CONECT   24   22   11   25                                                  
CONECT   25   24   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   10    7   28                                             
CONECT   28   27                                                            
CONECT   29    4   30                                                       
CONECT   30   29   31   32                                                  
CONECT   31   30                                                            
CONECT   32   30    2   33                                                  
CONECT   33   32                                                            
MASTER        0    0    0    0    0    0    0    0   33    0   76    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₈H₄₀O₅

Average Mass

456.6230 Da

Monoisotopic Mass

456.28757 Da

IUPAC Name

(1S,2R,6S,7R,9R,11S,12S,15R,16S)-15-[(1S)-1-[(2S,4S,5R)-4,5-dimethyl-6-oxooxan-2-yl]ethyl]-6-hydroxy-2,16-dimethyl-8-oxapentacyclo[9.7.0.0^{2,7}.0^{7,9}.0^{12,16}]octadec-4-en-3-one

Traditional Name

(1S,2R,6S,7R,9R,11S,12S,15R,16S)-15-[(1S)-1-[(2S,4S,5R)-4,5-dimethyl-6-oxooxan-2-yl]ethyl]-6-hydroxy-2,16-dimethyl-8-oxapentacyclo[9.7.0.0^{2,7}.0^{7,9}.0^{12,16}]octadec-4-en-3-one

CAS Registry Number

Not Available

SMILES

C[C@@H]([C@H]1CC[C@H]2[C@@H]3C[C@H]4O[C@]44[C@@H](O)C=CC(=O)[C@]4(C)[C@H]3CC[C@]12C)[C@@H]1C[C@H](C)[C@@H](C)C(=O)O1

InChI Identifier

InChI=1S/C28H40O5/c1-14-12-21(32-25(31)15(14)2)16(3)18-6-7-19-17-13-24-28(33-24)23(30)9-8-22(29)27(28,5)20(17)10-11-26(18,19)4/h8-9,14-21,23-24,30H,6-7,10-13H2,1-5H3/t14-,15+,16-,17-,18+,19-,20-,21-,23-,24+,26+,27-,28+/m0/s1

InChI Key

RXCZYUYRSCOXSS-NIWYTSODSA-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
Withania somnifera	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as withanolides and derivatives. These are c28 steroids structurally characterized by an ergostane skeleton usually functionalized at carbons 1, 22 and 26 to form a lactone ring.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Steroids and steroid derivatives

Sub Class

Steroid lactones

Direct Parent

Withanolides and derivatives

Alternative Parents

Substituents

Withanolide-skeleton
5,6-epoxysteroid
Delta valerolactone
Cyclohexenone
Delta_valerolactone
Oxepane
Oxane
Carboxylic acid ester
Ketone
Lactone
Secondary alcohol
Carboxylic acid derivative
Dialkyl ether
Oxirane
Ether
Oxacycle
Organoheterocyclic compound
Monocarboxylic acid or derivatives
Carbonyl group
Alcohol
Hydrocarbon derivative
Organic oxygen compound
Organic oxide
Organooxygen compound
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	4.82	ChemAxon
pKa (Strongest Acidic)	13.44	ChemAxon
pKa (Strongest Basic)	-3.5	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	76.13 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	124.81 m³·mol⁻¹	ChemAxon
Polarizability	52.39 Å³	ChemAxon
Number of Rings	6	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

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

162995147

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,6s,7r,9r,11s,12s,15r,16s)-15-[(1s)-1-[(2s,4s,5r)-4,5-dimethyl-6-oxooxan-2-yl]ethyl]-6-hydroxy-2,16-dimethyl-8-oxapentacyclo[9.7.0.0²,⁷.0⁷,⁹.0¹²,¹⁶]octadec-4-en-3-one (NP0313596)

MOL for NP0313596 ((1s,2r,6s,7r,9r,11s,12s,15r,16s)-15-[(1s)-1-[(2s,4s,5r)-4,5-dimethyl-6-oxooxan-2-yl]ethyl]-6-hydroxy-2,16-dimethyl-8-oxapentacyclo[9.7.0.0²,⁷.0⁷,⁹.0¹²,¹⁶]octadec-4-en-3-one)

3D MOL for NP0313596 ((1s,2r,6s,7r,9r,11s,12s,15r,16s)-15-[(1s)-1-[(2s,4s,5r)-4,5-dimethyl-6-oxooxan-2-yl]ethyl]-6-hydroxy-2,16-dimethyl-8-oxapentacyclo[9.7.0.0²,⁷.0⁷,⁹.0¹²,¹⁶]octadec-4-en-3-one)

3D SDF for NP0313596 ((1s,2r,6s,7r,9r,11s,12s,15r,16s)-15-[(1s)-1-[(2s,4s,5r)-4,5-dimethyl-6-oxooxan-2-yl]ethyl]-6-hydroxy-2,16-dimethyl-8-oxapentacyclo[9.7.0.0²,⁷.0⁷,⁹.0¹²,¹⁶]octadec-4-en-3-one)

3D-SDF for NP0313596 ((1s,2r,6s,7r,9r,11s,12s,15r,16s)-15-[(1s)-1-[(2s,4s,5r)-4,5-dimethyl-6-oxooxan-2-yl]ethyl]-6-hydroxy-2,16-dimethyl-8-oxapentacyclo[9.7.0.0²,⁷.0⁷,⁹.0¹²,¹⁶]octadec-4-en-3-one)

PDB for NP0313596 ((1s,2r,6s,7r,9r,11s,12s,15r,16s)-15-[(1s)-1-[(2s,4s,5r)-4,5-dimethyl-6-oxooxan-2-yl]ethyl]-6-hydroxy-2,16-dimethyl-8-oxapentacyclo[9.7.0.0²,⁷.0⁷,⁹.0¹²,¹⁶]octadec-4-en-3-one)

3D PDB for NP0313596 ((1s,2r,6s,7r,9r,11s,12s,15r,16s)-15-[(1s)-1-[(2s,4s,5r)-4,5-dimethyl-6-oxooxan-2-yl]ethyl]-6-hydroxy-2,16-dimethyl-8-oxapentacyclo[9.7.0.0²,⁷.0⁷,⁹.0¹²,¹⁶]octadec-4-en-3-one)

SMILES for NP0313596 ((1s,2r,6s,7r,9r,11s,12s,15r,16s)-15-[(1s)-1-[(2s,4s,5r)-4,5-dimethyl-6-oxooxan-2-yl]ethyl]-6-hydroxy-2,16-dimethyl-8-oxapentacyclo[9.7.0.0²,⁷.0⁷,⁹.0¹²,¹⁶]octadec-4-en-3-one)

INCHI for NP0313596 ((1s,2r,6s,7r,9r,11s,12s,15r,16s)-15-[(1s)-1-[(2s,4s,5r)-4,5-dimethyl-6-oxooxan-2-yl]ethyl]-6-hydroxy-2,16-dimethyl-8-oxapentacyclo[9.7.0.0²,⁷.0⁷,⁹.0¹²,¹⁶]octadec-4-en-3-one)

Structure for NP0313596 ((1s,2r,6s,7r,9r,11s,12s,15r,16s)-15-[(1s)-1-[(2s,4s,5r)-4,5-dimethyl-6-oxooxan-2-yl]ethyl]-6-hydroxy-2,16-dimethyl-8-oxapentacyclo[9.7.0.0²,⁷.0⁷,⁹.0¹²,¹⁶]octadec-4-en-3-one)

3D Structure for NP0313596 ((1s,2r,6s,7r,9r,11s,12s,15r,16s)-15-[(1s)-1-[(2s,4s,5r)-4,5-dimethyl-6-oxooxan-2-yl]ethyl]-6-hydroxy-2,16-dimethyl-8-oxapentacyclo[9.7.0.0²,⁷.0⁷,⁹.0¹²,¹⁶]octadec-4-en-3-one)