NP-MRD: Showing NP-Card for 2,3-Dihydro-3alpha-methoxynimbolide (NP0137889)

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Record Information

Version

2.0

Created at

2022-05-31 16:37:55 UTC

Updated at

2022-05-31 16:37:55 UTC

NP-MRD ID

NP0137889

Secondary Accession Numbers

None

Natural Product Identification

Common Name

2,3-Dihydro-3alpha-methoxynimbolide

Description

2,3-Dihydro-3alpha-methoxynimbolide belongs to the class of organic compounds known as limonoids. These are highly oxygenated, modified terpenoids with a prototypical structure either containing or derived from a precursor with a 4,4,8-trimethyl-17-furanylsteroid skeleton. All naturally occurring citrus limonoids contain a furan ring attached to the D-ring, at C-17, as well as oxygen containing functional groups at C-3, C-4, C-7, C-16 and C-17. 2,3-Dihydro-3alpha-methoxynimbolide was first documented in 2014 (PMID: 24706622). Based on a literature review very few articles have been published on 2,3-Dihydro-3alpha-methoxynimbolide.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652305312218372D          

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M  END

     RDKit          3D

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  Mrv1652305312218372D          

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    4.4019    3.6286    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1893    3.8750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7688    1.7433    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9491    2.5484    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7704    2.6257    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.0978    1.8685    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.4788    1.3231    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  6  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  1  0  0  0
  4  6  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  2  0  0  0  0
  2  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  1  0  0  0
  9 11  1  0  0  0  0
 11 12  1  1  0  0  0
 11 13  1  0  0  0  0
  2 13  1  0  0  0  0
 11 14  1  0  0  0  0
 14 15  1  1  0  0  0
 14 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
 17 19  1  0  0  0  0
 19 20  1  1  0  0  0
 19 21  1  0  0  0  0
 14 21  1  0  0  0  0
 21 22  1  6  0  0  0
 21 23  1  0  0  0  0
 23 24  1  1  0  0  0
 23 25  1  0  0  0  0
 25 26  2  0  0  0  0
 25 27  1  0  0  0  0
 27 28  1  0  0  0  0
 19 28  1  0  0  0  0
 28 29  1  1  0  0  0
 28 30  1  6  0  0  0
 30 31  1  0  0  0  0
 23 32  1  0  0  0  0
  9 32  1  0  0  0  0
 32 33  1  6  0  0  0
 32 34  1  1  0  0  0
 34 35  1  0  0  0  0
 35 36  2  0  0  0  0
 35 37  1  0  0  0  0
 37 38  1  0  0  0  0
  4 39  1  6  0  0  0
 39 40  2  0  0  0  0
 40 41  1  0  0  0  0
 41 42  1  0  0  0  0
 42 43  2  0  0  0  0
 39 43  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0137889

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@@]12C[C@]([H])(C(C)=C1[C@]1(C)[C@]([H])(O2)[C@]2([H])OC(=O)[C@@]3(C)[C@@]2([H])[C@](C)(C(=O)C[C@@]3([H])OC)[C@@]1([H])CC(=O)OC)C1=COC=C1

> <INCHI_IDENTIFIER>
InChI=1S/C28H34O8/c1-13-15(14-7-8-34-12-14)9-16-21(13)27(3)17(10-20(30)33-6)26(2)18(29)11-19(32-5)28(4)23(26)22(24(27)35-16)36-25(28)31/h7-8,12,15-17,19,22-24H,9-11H2,1-6H3/t15-,16-,17-,19-,22-,23-,24-,26+,27-,28-/m1/s1

> <INCHI_KEY>
OROAUBFPFAPQMD-LPLKPKLGSA-N

> <FORMULA>
C28H34O8

> <MOLECULAR_WEIGHT>
498.572

> <EXACT_MASS>
498.225368055

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
70

> <JCHEM_AVERAGE_POLARIZABILITY>
52.07927760803865

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
methyl 2-[(1R,2S,4R,6R,9R,10S,11R,14R,15S,18R)-6-(furan-3-yl)-14-methoxy-7,9,11,15-tetramethyl-12,16-dioxo-3,17-dioxapentacyclo[9.6.1.0^{2,9}.0^{4,8}.0^{15,18}]octadec-7-en-10-yl]acetate

> <JCHEM_LOGP>
2.7143656036666655

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
17.034677778901095

> <JCHEM_PKA_STRONGEST_BASIC>
-2.837018301844371

> <JCHEM_POLAR_SURFACE_AREA>
101.27000000000001

> <JCHEM_REFRACTIVITY>
126.88429999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
methyl [(1R,2S,4R,6R,9R,10S,11R,14R,15S,18R)-6-(furan-3-yl)-14-methoxy-7,9,11,15-tetramethyl-12,16-dioxo-3,17-dioxapentacyclo[9.6.1.0^{2,9}.0^{4,8}.0^{15,18}]octadec-7-en-10-yl]acetate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 31-MAY-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   31-MAY-22         0                                  
HETATM    1  H   UNK     0       9.963  -0.418   0.000  0.00  0.00           H+0
HETATM    2  C   UNK     0       9.352   0.996   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      10.885   1.140   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      11.222   2.643   0.000  0.00  0.00           C+0
HETATM    5  H   UNK     0      11.319   4.180   0.000  0.00  0.00           H+0
HETATM    6  C   UNK     0       9.896   3.427   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       9.752   4.961   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       8.741   2.409   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       7.208   2.265   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       7.699   3.724   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       6.871   0.762   0.000  0.00  0.00           C+0
HETATM   12  H   UNK     0       6.694  -0.768   0.000  0.00  0.00           H+0
HETATM   13  O   UNK     0       8.196  -0.022   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       5.401   0.302   0.000  0.00  0.00           C+0
HETATM   15  H   UNK     0       5.738   1.805   0.000  0.00  0.00           H+0
HETATM   16  O   UNK     0       4.760  -1.098   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       3.230  -0.920   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       2.187  -2.053   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       2.926   0.589   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       1.671  -0.302   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       4.268   1.345   0.000  0.00  0.00           C+0
HETATM   22  H   UNK     0       3.032   2.264   0.000  0.00  0.00           H+0
HETATM   23  C   UNK     0       4.605   2.848   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       4.728   4.383   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       2.960   3.669   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       2.921   5.209   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0       1.618   2.914   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       1.601   1.374   0.000  0.00  0.00           C+0
HETATM   29  H   UNK     0       0.276   2.158   0.000  0.00  0.00           H+0
HETATM   30  O   UNK     0       0.259   0.618   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0      -1.066   1.403   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       6.074   3.308   0.000  0.00  0.00           C+0
HETATM   33  H   UNK     0       7.146   4.413   0.000  0.00  0.00           H+0
HETATM   34  C   UNK     0       6.411   4.811   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       7.880   5.271   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0       9.014   4.228   0.000  0.00  0.00           O+0
HETATM   37  O   UNK     0       8.217   6.773   0.000  0.00  0.00           O+0
HETATM   38  C   UNK     0       9.687   7.233   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0      12.635   3.254   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0      12.972   4.757   0.000  0.00  0.00           C+0
HETATM   41  O   UNK     0      14.505   4.901   0.000  0.00  0.00           O+0
HETATM   42  C   UNK     0      15.116   3.488   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0      13.960   2.470   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    8   13                                             
CONECT    3    2    4                                                       
CONECT    4    3    5    6   39                                             
CONECT    5    4                                                            
CONECT    6    4    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    2    9                                                  
CONECT    9    8   10   11   32                                             
CONECT   10    9                                                            
CONECT   11    9   12   13   14                                             
CONECT   12   11                                                            
CONECT   13   11    2                                                       
CONECT   14   11   15   16   21                                             
CONECT   15   14                                                            
CONECT   16   14   17                                                       
CONECT   17   16   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   20   21   28                                             
CONECT   20   19                                                            
CONECT   21   19   14   22   23                                             
CONECT   22   21                                                            
CONECT   23   21   24   25   32                                             
CONECT   24   23                                                            
CONECT   25   23   26   27                                                  
CONECT   26   25                                                            
CONECT   27   25   28                                                       
CONECT   28   27   19   29   30                                             
CONECT   29   28                                                            
CONECT   30   28   31                                                       
CONECT   31   30                                                            
CONECT   32   23    9   33   34                                             
CONECT   33   32                                                            
CONECT   34   32   35                                                       
CONECT   35   34   36   37                                                  
CONECT   36   35                                                            
CONECT   37   35   38                                                       
CONECT   38   37                                                            
CONECT   39    4   40   43                                                  
CONECT   40   39   41                                                       
CONECT   41   40   42                                                       
CONECT   42   41   43                                                       
CONECT   43   42   39                                                       
MASTER        0    0    0    0    0    0    0    0   43    0   96    0
END

View in JSmol

Synonyms

Value	Source
2,3-Dihydro-3a-methoxynimbolide	Generator
2,3-Dihydro-3α-methoxynimbolide	Generator

Chemical Formula

C₂₈H₃₄O₈

Average Mass

498.5720 Da

Monoisotopic Mass

498.22537 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

1607828-35-2

SMILES

[H][C@@]12C[C@]([H])(C(C)=C1[C@]1(C)[C@]([H])(O2)[C@]2([H])OC(=O)[C@@]3(C)[C@@]2([H])[C@](C)(C(=O)C[C@@]3([H])OC)[C@@]1([H])CC(=O)OC)C1=COC=C1

InChI Identifier

InChI=1S/C28H34O8/c1-13-15(14-7-8-34-12-14)9-16-21(13)27(3)17(10-20(30)33-6)26(2)18(29)11-19(32-5)28(4)23(26)22(24(27)35-16)36-25(28)31/h7-8,12,15-17,19,22-24H,9-11H2,1-6H3/t15-,16-,17-,19-,22-,23-,24-,26+,27-,28-/m1/s1

InChI Key

OROAUBFPFAPQMD-LPLKPKLGSA-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

Not Available

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as limonoids. These are highly oxygenated, modified terpenoids with a prototypical structure either containing or derived from a precursor with a 4,4,8-trimethyl-17-furanylsteroid skeleton. All naturally occurring citrus limonoids contain a furan ring attached to the D-ring, at C-17, as well as oxygen containing functional groups at C-3, C-4, C-7, C-16 and C-17.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Triterpenoids

Direct Parent

Limonoids

Alternative Parents

Substituents

Limonoid skeleton
Naphthofuran
Gamma butyrolactone
Dicarboxylic acid or derivatives
Heteroaromatic compound
Methyl ester
Tetrahydrofuran
Furan
Lactone
Ketone
Carboxylic acid ester
Oxacycle
Organoheterocyclic compound
Ether
Dialkyl ether
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic 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

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

62782623

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

102200378

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Manosroi A, Kitdamrongtham W, Ishii K, Shinozaki T, Tachi Y, Takagi M, Ebina K, Zhang J, Manosroi J, Akihisa R, Akihisa T: Limonoids from Azadirachta indica var. siamensis extracts and their cytotoxic and melanogenesis-inhibitory activities. Chem Biodivers. 2014 Apr;11(4):505-31. doi: 10.1002/cbdv.201300406. [PubMed:24706622 ]

Showing NP-Card for 2,3-Dihydro-3alpha-methoxynimbolide (NP0137889)

MOL for NP0137889 (2,3-Dihydro-3alpha-methoxynimbolide)

3D MOL for NP0137889 (2,3-Dihydro-3alpha-methoxynimbolide)

3D SDF for NP0137889 (2,3-Dihydro-3alpha-methoxynimbolide)

3D-SDF for NP0137889 (2,3-Dihydro-3alpha-methoxynimbolide)

PDB for NP0137889 (2,3-Dihydro-3alpha-methoxynimbolide)

3D PDB for NP0137889 (2,3-Dihydro-3alpha-methoxynimbolide)

SMILES for NP0137889 (2,3-Dihydro-3alpha-methoxynimbolide)

INCHI for NP0137889 (2,3-Dihydro-3alpha-methoxynimbolide)

Structure for NP0137889 (2,3-Dihydro-3alpha-methoxynimbolide)

3D Structure for NP0137889 (2,3-Dihydro-3alpha-methoxynimbolide)