NP-MRD: Showing NP-Card for (1r,2r,5s,6r,9s,12s,13r)-6-[(2r)-4,5-dimethyl-6-oxo-2,3-dihydropyran-2-yl]-2-hydroxy-6,13-dimethyl-7-oxapentacyclo[10.8.0.0²,⁹.0⁵,⁹.0¹³,¹⁸]icosa-16,18-diene-8,14-dione (NP0308696)

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Record Information

Version

2.0

Created at

2022-09-11 02:40:33 UTC

Updated at

2022-09-11 02:40:33 UTC

NP-MRD ID

NP0308696

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1r,2r,5s,6r,9s,12s,13r)-6-[(2r)-4,5-dimethyl-6-oxo-2,3-dihydropyran-2-yl]-2-hydroxy-6,13-dimethyl-7-oxapentacyclo[10.8.0.0²,⁹.0⁵,⁹.0¹³,¹⁸]icosa-16,18-diene-8,14-dione

Description

Withaphysalin D 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. (1r,2r,5s,6r,9s,12s,13r)-6-[(2r)-4,5-dimethyl-6-oxo-2,3-dihydropyran-2-yl]-2-hydroxy-6,13-dimethyl-7-oxapentacyclo[10.8.0.0²,⁹.0⁵,⁹.0¹³,¹⁸]icosa-16,18-diene-8,14-dione is found in Physalis minima. (1r,2r,5s,6r,9s,12s,13r)-6-[(2r)-4,5-dimethyl-6-oxo-2,3-dihydropyran-2-yl]-2-hydroxy-6,13-dimethyl-7-oxapentacyclo[10.8.0.0²,⁹.0⁵,⁹.0¹³,¹⁸]icosa-16,18-diene-8,14-dione was first documented in 2016 (PMID: 27382976). Based on a literature review a small amount of articles have been published on Withaphysalin D (PMID: 33840171).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309112204402D          

 34 39  0  0  1  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652309112204402D          

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 17 27  1  0  0  0  0
 27 28  1  6  0  0  0
 18 29  1  0  0  0  0
 14 29  1  0  0  0  0
 29 30  1  1  0  0  0
 29 31  1  0  0  0  0
 31 32  1  0  0  0  0
 33 32  1  6  0  0  0
 14 33  1  0  0  0  0
  9 33  1  0  0  0  0
  8 34  1  0  0  0  0
  2 34  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0308696

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC1=C(C)C(=O)O[C@H](C1)[C@]1(C)OC(=O)[C@]23CC[C@H]4[C@@H](CC=C5C=CCC(=O)[C@]45C)[C@]2(O)CC[C@H]13

> <INCHI_IDENTIFIER>
InChI=1S/C28H34O6/c1-15-14-22(33-23(30)16(15)2)26(4)20-11-13-28(32)19-9-8-17-6-5-7-21(29)25(17,3)18(19)10-12-27(20,28)24(31)34-26/h5-6,8,18-20,22,32H,7,9-14H2,1-4H3/t18-,19+,20+,22+,25-,26+,27+,28+/m0/s1

> <INCHI_KEY>
LNINXSFPCHLADE-UENQGIQXSA-N

> <FORMULA>
C28H34O6

> <MOLECULAR_WEIGHT>
466.574

> <EXACT_MASS>
466.235538815

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
68

> <JCHEM_AVERAGE_POLARIZABILITY>
51.153935385371575

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1R,2R,5S,6R,9S,12S,13R)-6-[(2R)-4,5-dimethyl-6-oxo-3,6-dihydro-2H-pyran-2-yl]-2-hydroxy-6,13-dimethyl-7-oxapentacyclo[10.8.0.0^{2,9}.0^{5,9}.0^{13,18}]icosa-16,18-diene-8,14-dione

> <JCHEM_LOGP>
3.7823882436666656

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.367677005970155

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.87700544122956

> <JCHEM_PKA_STRONGEST_BASIC>
-3.2835120908850666

> <JCHEM_POLAR_SURFACE_AREA>
89.9

> <JCHEM_REFRACTIVITY>
126.83349999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1R,2R,5S,6R,9S,12S,13R)-6-[(2R)-4,5-dimethyl-6-oxo-2,3-dihydropyran-2-yl]-2-hydroxy-6,13-dimethyl-7-oxapentacyclo[10.8.0.0^{2,9}.0^{5,9}.0^{13,18}]icosa-16,18-diene-8,14-dione

> <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      -3.772   0.519   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -2.316   1.020   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -2.022   2.532   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -3.185   3.542   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.566   3.033   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -0.272   4.545   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       0.596   2.023   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       0.302   0.511   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.465  -0.499   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.339  -1.549   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       2.348   0.763   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       3.821   0.313   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       5.051   1.240   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       3.848  -1.227   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       4.449   0.190   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       5.978   0.378   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       6.905  -0.852   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       6.303  -2.269   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       7.230  -3.499   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       8.759  -3.311   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       9.360  -1.894   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      10.889  -1.706   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      11.490  -0.288   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      10.563   0.942   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       9.035   0.754   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       8.108   1.984   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0       8.433  -0.664   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       7.506   0.566   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       4.775  -2.457   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0       5.568  -3.777   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0       3.892  -3.719   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       2.419  -3.268   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       2.392  -1.729   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      -1.154   0.010   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   34                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8                                                       
CONECT    8    7    9   34                                                  
CONECT    9    8   10   11   33                                             
CONECT   10    9                                                            
CONECT   11    9   12                                                       
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12   15   29   33                                             
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18   27                                                  
CONECT   18   17   19   29                                                  
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   22   27                                                  
CONECT   22   21   23                                                       
CONECT   23   22   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24   26   27                                                  
CONECT   26   25                                                            
CONECT   27   25   21   17   28                                             
CONECT   28   27                                                            
CONECT   29   18   14   30   31                                             
CONECT   30   29                                                            
CONECT   31   29   32                                                       
CONECT   32   31   33                                                       
CONECT   33   32   14    9                                                  
CONECT   34    8    2                                                       
MASTER        0    0    0    0    0    0    0    0   34    0   78    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₈H₃₄O₆

Average Mass

466.5740 Da

Monoisotopic Mass

466.23554 Da

IUPAC Name

(1R,2R,5S,6R,9S,12S,13R)-6-[(2R)-4,5-dimethyl-6-oxo-3,6-dihydro-2H-pyran-2-yl]-2-hydroxy-6,13-dimethyl-7-oxapentacyclo[10.8.0.0^{2,9}.0^{5,9}.0^{13,18}]icosa-16,18-diene-8,14-dione

Traditional Name

(1R,2R,5S,6R,9S,12S,13R)-6-[(2R)-4,5-dimethyl-6-oxo-2,3-dihydropyran-2-yl]-2-hydroxy-6,13-dimethyl-7-oxapentacyclo[10.8.0.0^{2,9}.0^{5,9}.0^{13,18}]icosa-16,18-diene-8,14-dione

CAS Registry Number

Not Available

SMILES

CC1=C(C)C(=O)O[C@H](C1)[C@]1(C)OC(=O)[C@]23CC[C@H]4[C@@H](CC=C5C=CCC(=O)[C@]45C)[C@]2(O)CC[C@H]13

InChI Identifier

InChI=1S/C28H34O6/c1-15-14-22(33-23(30)16(15)2)26(4)20-11-13-28(32)19-9-8-17-6-5-7-21(29)25(17,3)18(19)10-12-27(20,28)24(31)34-26/h5-6,8,18-20,22,32H,7,9-14H2,1-4H3/t18-,19+,20+,22+,25-,26+,27+,28+/m0/s1

InChI Key

LNINXSFPCHLADE-UENQGIQXSA-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
Physalis minima	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
14-hydroxysteroid
Hydroxysteroid
1-oxosteroid
Oxosteroid
Dihydropyranone
Cyclohexenone
Pyran
Gamma butyrolactone
Dicarboxylic acid or derivatives
Enoate ester
Tetrahydrofuran
Tertiary alcohol
Alpha,beta-unsaturated carboxylic ester
Cyclic alcohol
Lactone
Ketone
Carboxylic acid ester
Oxacycle
Organoheterocyclic compound
Carboxylic acid derivative
Hydrocarbon derivative
Alcohol
Organic oxygen compound
Organic oxide
Organooxygen compound
Carbonyl group
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	3.78	ChemAxon
pKa (Strongest Acidic)	13.88	ChemAxon
pKa (Strongest Basic)	-3.3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	89.9 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	126.83 m³·mol⁻¹	ChemAxon
Polarizability	51.15 Å³	ChemAxon
Number of Rings	6	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	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

101293641

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Rath SN, Jena L, Bhuyan R, Mahanandia NC, Patri M: In silico discovery and evaluation of phytochemicals binding mechanism against human catechol-O-methyltransferase as a putative bioenhancer of L-DOPA therapy in Parkinson disease. Genomics Inform. 2021 Mar;19(1):e7. doi: 10.5808/gi.20061. Epub 2021 Feb 26. [PubMed:33840171 ]
Rao PC, Begum S, Jahromi MA, Jahromi ZH, Sriram S, Sahai M: Cytotoxicity of withasteroids: withametelin induces cell cycle arrest at G2/M phase and mitochondria-mediated apoptosis in non-small cell lung cancer A549 cells. Tumour Biol. 2016 Sep;37(9):12579-12587. doi: 10.1007/s13277-016-5128-5. Epub 2016 Jul 6. [PubMed:27382976 ]
LOTUS database [Link]

Showing NP-Card for (1r,2r,5s,6r,9s,12s,13r)-6-[(2r)-4,5-dimethyl-6-oxo-2,3-dihydropyran-2-yl]-2-hydroxy-6,13-dimethyl-7-oxapentacyclo[10.8.0.0²,⁹.0⁵,⁹.0¹³,¹⁸]icosa-16,18-diene-8,14-dione (NP0308696)

MOL for NP0308696 ((1r,2r,5s,6r,9s,12s,13r)-6-[(2r)-4,5-dimethyl-6-oxo-2,3-dihydropyran-2-yl]-2-hydroxy-6,13-dimethyl-7-oxapentacyclo[10.8.0.0²,⁹.0⁵,⁹.0¹³,¹⁸]icosa-16,18-diene-8,14-dione)

3D MOL for NP0308696 ((1r,2r,5s,6r,9s,12s,13r)-6-[(2r)-4,5-dimethyl-6-oxo-2,3-dihydropyran-2-yl]-2-hydroxy-6,13-dimethyl-7-oxapentacyclo[10.8.0.0²,⁹.0⁵,⁹.0¹³,¹⁸]icosa-16,18-diene-8,14-dione)

3D SDF for NP0308696 ((1r,2r,5s,6r,9s,12s,13r)-6-[(2r)-4,5-dimethyl-6-oxo-2,3-dihydropyran-2-yl]-2-hydroxy-6,13-dimethyl-7-oxapentacyclo[10.8.0.0²,⁹.0⁵,⁹.0¹³,¹⁸]icosa-16,18-diene-8,14-dione)

3D-SDF for NP0308696 ((1r,2r,5s,6r,9s,12s,13r)-6-[(2r)-4,5-dimethyl-6-oxo-2,3-dihydropyran-2-yl]-2-hydroxy-6,13-dimethyl-7-oxapentacyclo[10.8.0.0²,⁹.0⁵,⁹.0¹³,¹⁸]icosa-16,18-diene-8,14-dione)

PDB for NP0308696 ((1r,2r,5s,6r,9s,12s,13r)-6-[(2r)-4,5-dimethyl-6-oxo-2,3-dihydropyran-2-yl]-2-hydroxy-6,13-dimethyl-7-oxapentacyclo[10.8.0.0²,⁹.0⁵,⁹.0¹³,¹⁸]icosa-16,18-diene-8,14-dione)

3D PDB for NP0308696 ((1r,2r,5s,6r,9s,12s,13r)-6-[(2r)-4,5-dimethyl-6-oxo-2,3-dihydropyran-2-yl]-2-hydroxy-6,13-dimethyl-7-oxapentacyclo[10.8.0.0²,⁹.0⁵,⁹.0¹³,¹⁸]icosa-16,18-diene-8,14-dione)

SMILES for NP0308696 ((1r,2r,5s,6r,9s,12s,13r)-6-[(2r)-4,5-dimethyl-6-oxo-2,3-dihydropyran-2-yl]-2-hydroxy-6,13-dimethyl-7-oxapentacyclo[10.8.0.0²,⁹.0⁵,⁹.0¹³,¹⁸]icosa-16,18-diene-8,14-dione)

INCHI for NP0308696 ((1r,2r,5s,6r,9s,12s,13r)-6-[(2r)-4,5-dimethyl-6-oxo-2,3-dihydropyran-2-yl]-2-hydroxy-6,13-dimethyl-7-oxapentacyclo[10.8.0.0²,⁹.0⁵,⁹.0¹³,¹⁸]icosa-16,18-diene-8,14-dione)

Structure for NP0308696 ((1r,2r,5s,6r,9s,12s,13r)-6-[(2r)-4,5-dimethyl-6-oxo-2,3-dihydropyran-2-yl]-2-hydroxy-6,13-dimethyl-7-oxapentacyclo[10.8.0.0²,⁹.0⁵,⁹.0¹³,¹⁸]icosa-16,18-diene-8,14-dione)

3D Structure for NP0308696 ((1r,2r,5s,6r,9s,12s,13r)-6-[(2r)-4,5-dimethyl-6-oxo-2,3-dihydropyran-2-yl]-2-hydroxy-6,13-dimethyl-7-oxapentacyclo[10.8.0.0²,⁹.0⁵,⁹.0¹³,¹⁸]icosa-16,18-diene-8,14-dione)