NP-MRD: Showing NP-Card for methyl 13-(furan-3-yl)-2-hydroxy-9-(2-methoxy-2-oxoethyl)-4,8,10,12-tetramethyl-7-oxo-16-oxatetracyclo[8.6.0.0³,⁸.0¹¹,¹⁵]hexadeca-5,11-diene-4-carboxylate (NP0194329)

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Record Information

Version

2.0

Created at

2022-09-04 11:57:54 UTC

Updated at

2022-09-04 11:57:54 UTC

NP-MRD ID

NP0194329

Secondary Accession Numbers

None

Natural Product Identification

Common Name

methyl 13-(furan-3-yl)-2-hydroxy-9-(2-methoxy-2-oxoethyl)-4,8,10,12-tetramethyl-7-oxo-16-oxatetracyclo[8.6.0.0³,⁸.0¹¹,¹⁵]hexadeca-5,11-diene-4-carboxylate

Description

Desacetylnimbin 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. methyl 13-(furan-3-yl)-2-hydroxy-9-(2-methoxy-2-oxoethyl)-4,8,10,12-tetramethyl-7-oxo-16-oxatetracyclo[8.6.0.0³,⁸.0¹¹,¹⁵]hexadeca-5,11-diene-4-carboxylate is found in Azadirachta indica. Desacetylnimbin is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1533004251506092D          

 36 40  0  0  0  0            999 V2000
    2.7166    3.3997    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3447    2.8648    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1955    2.0534    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8236    1.5185    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4182    1.7769    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2690    0.9655    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8971    0.4306    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1303    1.2219    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7479   -0.3808    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4735   -0.7735    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0712   -0.2047    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    3.7149    0.5394    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END

     RDKit          3D

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M  END


  Mrv1533004251506092D          

 36 40  0  0  0  0            999 V2000
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 17 18  2  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  2  0  0  0  0
 17 21  1  0  0  0  0
  9 22  1  0  0  0  0
 22 23  1  0  0  0  0
 22 24  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  1  0  0  0  0
 25 27  1  0  0  0  0
 27 28  2  0  0  0  0
 28 29  1  0  0  0  0
 29 30  2  0  0  0  0
 29 31  1  0  0  0  0
  6 31  1  0  0  0  0
 24 31  1  0  0  0  0
 31 32  1  0  0  0  0
 25 33  1  0  0  0  0
 33 34  2  0  0  0  0
 33 35  1  0  0  0  0
 35 36  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0194329

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC(=O)CC1C2(C)C(OC3CC(C(C)=C23)C2=COC=C2)C(O)C2C(C)(C=CC(=O)C12C)C(=O)OC

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

> <INCHI_KEY>
CTBHKOAPXBDFPX-UHFFFAOYSA-N

> <FORMULA>
C28H34O8

> <MOLECULAR_WEIGHT>
498.572

> <EXACT_MASS>
498.225368055

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
70

> <JCHEM_AVERAGE_POLARIZABILITY>
52.93122597064176

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
methyl 13-(furan-3-yl)-2-hydroxy-9-(2-methoxy-2-oxoethyl)-4,8,10,12-tetramethyl-7-oxo-16-oxatetracyclo[8.6.0.0³,⁸.0¹¹,¹⁵]hexadeca-5,11-diene-4-carboxylate

> <ALOGPS_LOGP>
3.26

> <JCHEM_LOGP>
2.625389127999999

> <ALOGPS_LOGS>
-4.00

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.84250764823162

> <JCHEM_PKA_STRONGEST_BASIC>
-2.8589972879293413

> <JCHEM_POLAR_SURFACE_AREA>
112.27

> <JCHEM_REFRACTIVITY>
130.1262

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.02e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
methyl 13-(furan-3-yl)-2-hydroxy-9-(2-methoxy-2-oxoethyl)-4,8,10,12-tetramethyl-7-oxo-16-oxatetracyclo[8.6.0.0³,⁸.0¹¹,¹⁵]hexadeca-5,11-diene-4-carboxylate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 25-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   25-APR-15         0                                  
HETATM    1  C   UNK     0       5.071   6.346   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       6.243   5.348   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       5.965   3.833   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       7.137   2.834   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       4.514   3.317   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.236   1.802   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       5.408   0.804   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       5.843   2.281   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       5.129  -0.711   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       6.484  -1.444   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       7.599  -0.382   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       9.126  -0.179   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       9.405   1.336   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       8.050   2.069   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       6.935   1.007   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       7.847   3.595   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      10.794   2.001   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      11.072   3.515   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      12.599   3.718   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0      13.264   2.329   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      12.148   1.268   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       3.679  -1.227   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0       3.400  -2.742   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0       2.506  -0.228   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       1.055  -0.745   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       1.815  -2.084   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      -0.117   0.254   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       0.161   1.768   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       1.612   2.285   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0       1.891   3.799   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0       2.785   1.286   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       3.063   2.801   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      -0.132  -1.726   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0       0.125  -3.244   0.000  0.00  0.00           O+0
HETATM   35  O   UNK     0      -1.575  -1.189   0.000  0.00  0.00           O+0
HETATM   36  C   UNK     0      -1.831   0.330   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6                                                       
CONECT    6    5    7   31                                                  
CONECT    7    6    8    9   15                                             
CONECT    8    7                                                            
CONECT    9    7   10   22                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12   15                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14   17                                                  
CONECT   14   13   15   16                                                  
CONECT   15   14    7   11                                                  
CONECT   16   14                                                            
CONECT   17   13   18   21                                                  
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   17                                                       
CONECT   22    9   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22   25   31                                                  
CONECT   25   24   26   27   33                                             
CONECT   26   25                                                            
CONECT   27   25   28                                                       
CONECT   28   27   29                                                       
CONECT   29   28   30   31                                                  
CONECT   30   29                                                            
CONECT   31   29    6   24   32                                             
CONECT   32   31                                                            
CONECT   33   25   34   35                                                  
CONECT   34   33                                                            
CONECT   35   33   36                                                       
CONECT   36   35                                                            
MASTER        0    0    0    0    0    0    0    0   36    0   80    0
END

View in JSmol

Synonyms

Value	Source
6-Desacetylnimbin	MeSH

Chemical Formula

C₂₈H₃₄O₈

Average Mass

498.5720 Da

Monoisotopic Mass

498.22537 Da

IUPAC Name

methyl 13-(furan-3-yl)-2-hydroxy-9-(2-methoxy-2-oxoethyl)-4,8,10,12-tetramethyl-7-oxo-16-oxatetracyclo[8.6.0.0³,⁸.0¹¹,¹⁵]hexadeca-5,11-diene-4-carboxylate

Traditional Name

methyl 13-(furan-3-yl)-2-hydroxy-9-(2-methoxy-2-oxoethyl)-4,8,10,12-tetramethyl-7-oxo-16-oxatetracyclo[8.6.0.0³,⁸.0¹¹,¹⁵]hexadeca-5,11-diene-4-carboxylate

CAS Registry Number

Not Available

SMILES

COC(=O)CC1C2(C)C(OC3CC(C(C)=C23)C2=COC=C2)C(O)C2C(C)(C=CC(=O)C12C)C(=O)OC

InChI Identifier

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

InChI Key

CTBHKOAPXBDFPX-UHFFFAOYSA-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
Azadirachta indica	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
Naphthofuran
Cyclohexenone
Dicarboxylic acid or derivatives
Cyclic alcohol
Heteroaromatic compound
Furan
Methyl ester
Tetrahydrofuran
Carboxylic acid ester
Ketone
Secondary alcohol
Carboxylic acid derivative
Dialkyl ether
Ether
Oxacycle
Organoheterocyclic compound
Organic oxide
Hydrocarbon derivative
Carbonyl group
Alcohol
Organic oxygen compound
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	3.26	ALOGPS
logP	2.63	ChemAxon
logS	-4	ALOGPS
pKa (Strongest Acidic)	13.84	ChemAxon
pKa (Strongest Basic)	-2.9	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	112.27 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	130.13 m³·mol⁻¹	ChemAxon
Polarizability	52.93 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	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

176996

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for methyl 13-(furan-3-yl)-2-hydroxy-9-(2-methoxy-2-oxoethyl)-4,8,10,12-tetramethyl-7-oxo-16-oxatetracyclo[8.6.0.0³,⁸.0¹¹,¹⁵]hexadeca-5,11-diene-4-carboxylate (NP0194329)

MOL for NP0194329 (methyl 13-(furan-3-yl)-2-hydroxy-9-(2-methoxy-2-oxoethyl)-4,8,10,12-tetramethyl-7-oxo-16-oxatetracyclo[8.6.0.0³,⁸.0¹¹,¹⁵]hexadeca-5,11-diene-4-carboxylate)

3D MOL for NP0194329 (methyl 13-(furan-3-yl)-2-hydroxy-9-(2-methoxy-2-oxoethyl)-4,8,10,12-tetramethyl-7-oxo-16-oxatetracyclo[8.6.0.0³,⁸.0¹¹,¹⁵]hexadeca-5,11-diene-4-carboxylate)

3D SDF for NP0194329 (methyl 13-(furan-3-yl)-2-hydroxy-9-(2-methoxy-2-oxoethyl)-4,8,10,12-tetramethyl-7-oxo-16-oxatetracyclo[8.6.0.0³,⁸.0¹¹,¹⁵]hexadeca-5,11-diene-4-carboxylate)

3D-SDF for NP0194329 (methyl 13-(furan-3-yl)-2-hydroxy-9-(2-methoxy-2-oxoethyl)-4,8,10,12-tetramethyl-7-oxo-16-oxatetracyclo[8.6.0.0³,⁸.0¹¹,¹⁵]hexadeca-5,11-diene-4-carboxylate)

PDB for NP0194329 (methyl 13-(furan-3-yl)-2-hydroxy-9-(2-methoxy-2-oxoethyl)-4,8,10,12-tetramethyl-7-oxo-16-oxatetracyclo[8.6.0.0³,⁸.0¹¹,¹⁵]hexadeca-5,11-diene-4-carboxylate)

3D PDB for NP0194329 (methyl 13-(furan-3-yl)-2-hydroxy-9-(2-methoxy-2-oxoethyl)-4,8,10,12-tetramethyl-7-oxo-16-oxatetracyclo[8.6.0.0³,⁸.0¹¹,¹⁵]hexadeca-5,11-diene-4-carboxylate)

SMILES for NP0194329 (methyl 13-(furan-3-yl)-2-hydroxy-9-(2-methoxy-2-oxoethyl)-4,8,10,12-tetramethyl-7-oxo-16-oxatetracyclo[8.6.0.0³,⁸.0¹¹,¹⁵]hexadeca-5,11-diene-4-carboxylate)

INCHI for NP0194329 (methyl 13-(furan-3-yl)-2-hydroxy-9-(2-methoxy-2-oxoethyl)-4,8,10,12-tetramethyl-7-oxo-16-oxatetracyclo[8.6.0.0³,⁸.0¹¹,¹⁵]hexadeca-5,11-diene-4-carboxylate)

Structure for NP0194329 (methyl 13-(furan-3-yl)-2-hydroxy-9-(2-methoxy-2-oxoethyl)-4,8,10,12-tetramethyl-7-oxo-16-oxatetracyclo[8.6.0.0³,⁸.0¹¹,¹⁵]hexadeca-5,11-diene-4-carboxylate)

3D Structure for NP0194329 (methyl 13-(furan-3-yl)-2-hydroxy-9-(2-methoxy-2-oxoethyl)-4,8,10,12-tetramethyl-7-oxo-16-oxatetracyclo[8.6.0.0³,⁸.0¹¹,¹⁵]hexadeca-5,11-diene-4-carboxylate)