NP-MRD: Showing NP-Card for (1s,2r,4s,7s,8s,11r,12s,17r,19r)-7-(furan-3-yl)-1,8,12,16,16-pentamethyl-5,10,15-trioxo-3,6-dioxapentacyclo[9.8.0.0²,⁴.0²,⁸.0¹²,¹⁷]nonadec-13-en-19-yl acetate (NP0253236)

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Record Information

Version

2.0

Created at

2022-09-07 17:03:08 UTC

Updated at

2022-09-07 17:03:08 UTC

NP-MRD ID

NP0253236

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1s,2r,4s,7s,8s,11r,12s,17r,19r)-7-(furan-3-yl)-1,8,12,16,16-pentamethyl-5,10,15-trioxo-3,6-dioxapentacyclo[9.8.0.0²,⁴.0²,⁸.0¹²,¹⁷]nonadec-13-en-19-yl acetate

Description

11-Oxogedunin 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. (1s,2r,4s,7s,8s,11r,12s,17r,19r)-7-(furan-3-yl)-1,8,12,16,16-pentamethyl-5,10,15-trioxo-3,6-dioxapentacyclo[9.8.0.0²,⁴.0²,⁸.0¹²,¹⁷]nonadec-13-en-19-yl acetate is found in Toona sinensis. (1s,2r,4s,7s,8s,11r,12s,17r,19r)-7-(furan-3-yl)-1,8,12,16,16-pentamethyl-5,10,15-trioxo-3,6-dioxapentacyclo[9.8.0.0²,⁴.0²,⁸.0¹²,¹⁷]nonadec-13-en-19-yl acetate was first documented in 2006 (PMID: 16989525). Based on a literature review very few articles have been published on 11-oxogedunin.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309072219032D          

 36 41  0  0  1  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652309072219032D          

 36 41  0  0  1  0            999 V2000
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 11 13  1  0  0  0  0
 13 14  2  0  0  0  0
 14 15  1  0  0  0  0
  7 15  1  0  0  0  0
 15 16  1  1  0  0  0
 15 17  1  0  0  0  0
 17 18  1  1  0  0  0
 18 19  2  0  0  0  0
 18 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  6  0  0  0
 21 23  1  0  0  0  0
 23 24  1  6  0  0  0
 24 25  1  0  0  0  0
 25 26  2  0  0  0  0
 26 27  1  0  0  0  0
 27 28  1  0  0  0  0
 24 28  2  0  0  0  0
 23 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
 32 33  1  1  0  0  0
 34 33  1  1  0  0  0
 32 34  1  0  0  0  0
 21 34  1  0  0  0  0
 34 35  1  0  0  0  0
  5 35  1  0  0  0  0
 17 35  1  0  0  0  0
 35 36  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0253236

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(=O)O[C@@H]1C[C@H]2C(C)(C)C(=O)C=C[C@]2(C)[C@H]2C(=O)C[C@@]3(C)[C@@H](OC(=O)[C@H]4O[C@@]34[C@]12C)C1=COC=C1

> <INCHI_IDENTIFIER>
InChI=1S/C28H32O8/c1-14(29)34-19-11-17-24(2,3)18(31)7-9-25(17,4)20-16(30)12-26(5)21(15-8-10-33-13-15)35-23(32)22-28(26,36-22)27(19,20)6/h7-10,13,17,19-22H,11-12H2,1-6H3/t17-,19+,20+,21-,22+,25-,26-,27+,28+/m0/s1

> <INCHI_KEY>
SPAMVCDESKNMPV-XBYNXRCNSA-N

> <FORMULA>
C28H32O8

> <MOLECULAR_WEIGHT>
496.556

> <EXACT_MASS>
496.20971799

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
68

> <JCHEM_AVERAGE_POLARIZABILITY>
50.455951769392954

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1S,2R,4S,7R,8S,11R,12S,17R,19R)-7-(furan-3-yl)-1,8,12,16,16-pentamethyl-5,10,15-trioxo-3,6-dioxapentacyclo[9.8.0.0^{2,4}.0^{2,8}.0^{12,17}]nonadec-13-en-19-yl acetate

> <JCHEM_LOGP>
3.3767337696666653

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
16.67205858731045

> <JCHEM_PKA_STRONGEST_BASIC>
-2.870147863211251

> <JCHEM_POLAR_SURFACE_AREA>
112.41000000000003

> <JCHEM_REFRACTIVITY>
125.66029999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1S,2R,4S,7R,8S,11R,12S,17R,19R)-7-(furan-3-yl)-1,8,12,16,16-pentamethyl-5,10,15-trioxo-3,6-dioxapentacyclo[9.8.0.0^{2,4}.0^{2,8}.0^{12,17}]nonadec-13-en-19-yl acetate

> <JCHEM_VEBER_RULE>
0

$$$$

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       5.870   5.718   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.358   5.427   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       3.350   6.591   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0       3.854   3.971   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       4.862   2.807   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.375   3.098   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       7.383   1.934   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       8.895   2.225   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       8.346   3.664   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      10.216   3.016   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       9.903   1.061   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      11.415   1.352   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       9.399  -0.394   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       7.887  -0.685   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       6.879   0.479   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       6.375  -0.976   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       5.366   0.188   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       4.862  -1.267   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       5.870  -2.431   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       3.350  -1.558   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       2.342  -0.394   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       1.838  -1.849   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       0.830  -0.685   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       0.326  -2.140   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       1.206  -3.403   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       0.277  -4.632   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0      -1.178  -4.128   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0      -1.148  -2.588   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0      -0.179   0.479   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0       0.326   1.934   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0      -0.683   3.098   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0       1.838   2.225   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0       3.350   2.516   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0       2.846   1.061   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       4.358   1.352   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0       4.227   2.886   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6   35                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8   15                                                  
CONECT    8    7    9   10   11                                             
CONECT    9    8                                                            
CONECT   10    8                                                            
CONECT   11    8   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14    7   16   17                                             
CONECT   16   15                                                            
CONECT   17   15   18   35                                                  
CONECT   18   17   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18   21                                                       
CONECT   21   20   22   23   34                                             
CONECT   22   21                                                            
CONECT   23   21   24   29                                                  
CONECT   24   23   25   28                                                  
CONECT   25   24   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   28                                                       
CONECT   28   27   24                                                       
CONECT   29   23   30                                                       
CONECT   30   29   31   32                                                  
CONECT   31   30                                                            
CONECT   32   30   33   34                                                  
CONECT   33   32   34                                                       
CONECT   34   33   32   21   35                                             
CONECT   35   34    5   17   36                                             
CONECT   36   35                                                            
MASTER        0    0    0    0    0    0    0    0   36    0   82    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₈H₃₂O₈

Average Mass

496.5560 Da

Monoisotopic Mass

496.20972 Da

IUPAC Name

(1S,2R,4S,7R,8S,11R,12S,17R,19R)-7-(furan-3-yl)-1,8,12,16,16-pentamethyl-5,10,15-trioxo-3,6-dioxapentacyclo[9.8.0.0^{2,4}.0^{2,8}.0^{12,17}]nonadec-13-en-19-yl acetate

Traditional Name

(1S,2R,4S,7R,8S,11R,12S,17R,19R)-7-(furan-3-yl)-1,8,12,16,16-pentamethyl-5,10,15-trioxo-3,6-dioxapentacyclo[9.8.0.0^{2,4}.0^{2,8}.0^{12,17}]nonadec-13-en-19-yl acetate

CAS Registry Number

Not Available

SMILES

CC(=O)O[C@@H]1C[C@H]2C(C)(C)C(=O)C=C[C@]2(C)[C@H]2C(=O)C[C@@]3(C)[C@@H](OC(=O)[C@H]4O[C@@]34[C@]12C)C1=COC=C1

InChI Identifier

InChI=1S/C28H32O8/c1-14(29)34-19-11-17-24(2,3)18(31)7-9-25(17,4)20-16(30)12-26(5)21(15-8-10-33-13-15)35-23(32)22-28(26,36-22)27(19,20)6/h7-10,13,17,19-22H,11-12H2,1-6H3/t17-,19+,20+,21-,22+,25-,26-,27+,28+/m0/s1

InChI Key

SPAMVCDESKNMPV-XBYNXRCNSA-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
Toona sinensis	LOTUS Database	35616633

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
Naphthopyran
Naphthalene
1,4-dioxepane
Delta valerolactone
Cyclohexenone
Dioxepane
Delta_valerolactone
Dicarboxylic acid or derivatives
Pyran
Oxane
Heteroaromatic compound
Furan
Carboxylic acid ester
Ketone
Cyclic ketone
Lactone
Organoheterocyclic compound
Ether
Oxirane
Oxacycle
Dialkyl ether
Carboxylic acid derivative
Hydrocarbon derivative
Organic oxide
Organic oxygen compound
Carbonyl group
Organooxygen compound
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
logP	3.38	ChemAxon
pKa (Strongest Acidic)	16.67	ChemAxon
pKa (Strongest Basic)	-2.9	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	112.41 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	125.66 m³·mol⁻¹	ChemAxon
Polarizability	50.46 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

10132589

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

11958342

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Mitsui K, Saito H, Yamamura R, Fukaya H, Hitotsuyanagi Y, Takeya K: Hydroxylated gedunin derivatives from Cedrela sinensis. J Nat Prod. 2006 Sep;69(9):1310-4. doi: 10.1021/np068021f. [PubMed:16989525 ]
LOTUS database [Link]

Showing NP-Card for (1s,2r,4s,7s,8s,11r,12s,17r,19r)-7-(furan-3-yl)-1,8,12,16,16-pentamethyl-5,10,15-trioxo-3,6-dioxapentacyclo[9.8.0.0²,⁴.0²,⁸.0¹²,¹⁷]nonadec-13-en-19-yl acetate (NP0253236)

MOL for NP0253236 ((1s,2r,4s,7s,8s,11r,12s,17r,19r)-7-(furan-3-yl)-1,8,12,16,16-pentamethyl-5,10,15-trioxo-3,6-dioxapentacyclo[9.8.0.0²,⁴.0²,⁸.0¹²,¹⁷]nonadec-13-en-19-yl acetate)

3D MOL for NP0253236 ((1s,2r,4s,7s,8s,11r,12s,17r,19r)-7-(furan-3-yl)-1,8,12,16,16-pentamethyl-5,10,15-trioxo-3,6-dioxapentacyclo[9.8.0.0²,⁴.0²,⁸.0¹²,¹⁷]nonadec-13-en-19-yl acetate)

3D SDF for NP0253236 ((1s,2r,4s,7s,8s,11r,12s,17r,19r)-7-(furan-3-yl)-1,8,12,16,16-pentamethyl-5,10,15-trioxo-3,6-dioxapentacyclo[9.8.0.0²,⁴.0²,⁸.0¹²,¹⁷]nonadec-13-en-19-yl acetate)

3D-SDF for NP0253236 ((1s,2r,4s,7s,8s,11r,12s,17r,19r)-7-(furan-3-yl)-1,8,12,16,16-pentamethyl-5,10,15-trioxo-3,6-dioxapentacyclo[9.8.0.0²,⁴.0²,⁸.0¹²,¹⁷]nonadec-13-en-19-yl acetate)

PDB for NP0253236 ((1s,2r,4s,7s,8s,11r,12s,17r,19r)-7-(furan-3-yl)-1,8,12,16,16-pentamethyl-5,10,15-trioxo-3,6-dioxapentacyclo[9.8.0.0²,⁴.0²,⁸.0¹²,¹⁷]nonadec-13-en-19-yl acetate)

3D PDB for NP0253236 ((1s,2r,4s,7s,8s,11r,12s,17r,19r)-7-(furan-3-yl)-1,8,12,16,16-pentamethyl-5,10,15-trioxo-3,6-dioxapentacyclo[9.8.0.0²,⁴.0²,⁸.0¹²,¹⁷]nonadec-13-en-19-yl acetate)

SMILES for NP0253236 ((1s,2r,4s,7s,8s,11r,12s,17r,19r)-7-(furan-3-yl)-1,8,12,16,16-pentamethyl-5,10,15-trioxo-3,6-dioxapentacyclo[9.8.0.0²,⁴.0²,⁸.0¹²,¹⁷]nonadec-13-en-19-yl acetate)

INCHI for NP0253236 ((1s,2r,4s,7s,8s,11r,12s,17r,19r)-7-(furan-3-yl)-1,8,12,16,16-pentamethyl-5,10,15-trioxo-3,6-dioxapentacyclo[9.8.0.0²,⁴.0²,⁸.0¹²,¹⁷]nonadec-13-en-19-yl acetate)

Structure for NP0253236 ((1s,2r,4s,7s,8s,11r,12s,17r,19r)-7-(furan-3-yl)-1,8,12,16,16-pentamethyl-5,10,15-trioxo-3,6-dioxapentacyclo[9.8.0.0²,⁴.0²,⁸.0¹²,¹⁷]nonadec-13-en-19-yl acetate)

3D Structure for NP0253236 ((1s,2r,4s,7s,8s,11r,12s,17r,19r)-7-(furan-3-yl)-1,8,12,16,16-pentamethyl-5,10,15-trioxo-3,6-dioxapentacyclo[9.8.0.0²,⁴.0²,⁸.0¹²,¹⁷]nonadec-13-en-19-yl acetate)