NP-MRD: Showing NP-Card for (+)-2,3-Dihydronimbolide (NP0082142)

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Record Information

Version

2.0

Created at

2022-04-29 03:11:57 UTC

Updated at

2022-04-29 03:11:57 UTC

NP-MRD ID

NP0082142

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(+)-2,3-Dihydronimbolide

Description

2,3-Dihydronimbolide 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-Dihydronimbolide is found in Azadirachta excelsa. (+)-2,3-Dihydronimbolide was first documented in 2018 (PMID: 30109187). Based on a literature review very few articles have been published on 2,3-dihydronimbolide (PMID: 31872594).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304292205112D          

 34 39  0  0  1  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652304292205112D          

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M  END
> <DATABASE_ID>
NP0082142

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC(=O)C[C@H]1[C@@]2(C)[C@H](O[C@@H]3C[C@H](C(C)=C23)C2=COC=C2)[C@@H]2OC(=O)[C@]3(C)CCC(=O)[C@@]1(C)[C@@H]23

> <INCHI_IDENTIFIER>
InChI=1S/C27H32O7/c1-13-15(14-7-9-32-12-14)10-16-20(13)27(4)17(11-19(29)31-5)26(3)18(28)6-8-25(2)22(26)21(23(27)33-16)34-24(25)30/h7,9,12,15-17,21-23H,6,8,10-11H2,1-5H3/t15-,16-,17-,21-,22+,23-,25-,26+,27-/m1/s1

> <INCHI_KEY>
IVORRUXZODBSHC-LSYMHUITSA-N

> <FORMULA>
C27H32O7

> <MOLECULAR_WEIGHT>
468.546

> <EXACT_MASS>
468.21480337

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
66

> <JCHEM_AVERAGE_POLARIZABILITY>
48.898705076657166

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
methyl 2-[(1R,2S,4R,6R,9R,10S,11R,15R,18R)-6-(furan-3-yl)-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

> <ALOGPS_LOGP>
3.67

> <JCHEM_LOGP>
3.146142706999999

> <ALOGPS_LOGS>
-3.89

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
18.84550100724589

> <JCHEM_PKA_STRONGEST_BASIC>
-2.859540534447446

> <JCHEM_POLAR_SURFACE_AREA>
92.04

> <JCHEM_REFRACTIVITY>
120.7716

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.08e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
methyl [(1R,2S,4R,6R,9R,10S,11R,15R,18R)-6-(furan-3-yl)-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                                 29-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   29-APR-22         0                                  
HETATM    1  C   UNK     0       6.820  -2.014   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       7.157  -0.512   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       6.023   0.531   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.554   0.071   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.217  -1.432   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       5.350  -2.474   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       4.709  -3.874   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       3.179  -3.697   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       2.136  -4.830   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       2.875  -2.187   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.550  -1.403   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       1.567   0.137   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       2.909   0.893   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       2.870   2.432   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       1.620  -3.079   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       4.677   1.606   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       6.360   2.034   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       5.227   3.077   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       3.757   2.617   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       5.563   4.580   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       4.430   5.622   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       8.690  -0.367   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       9.845   0.651   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      11.171  -0.134   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      10.834  -1.636   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       9.301  -1.781   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0       8.145  -2.799   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0      12.584   0.478   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      12.921   1.980   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      14.454   2.125   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0      15.065   0.711   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0      13.909  -0.307   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       9.701   2.184   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       7.648   0.948   0.000  0.00  0.00           C+0
CONECT    1    2    6   27                                                  
CONECT    2    1    3   22   34                                             
CONECT    3    2    4   17                                                  
CONECT    4    3    5   13   16                                             
CONECT    5    4    6   10                                                  
CONECT    6    5    1    7                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8    5   11   15                                             
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12    4   14                                                  
CONECT   14   13                                                            
CONECT   15   10                                                            
CONECT   16    4                                                            
CONECT   17    3   18                                                       
CONECT   18   17   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18   21                                                       
CONECT   21   20                                                            
CONECT   22    2   23   26                                                  
CONECT   23   22   24   33                                                  
CONECT   24   23   25   28                                                  
CONECT   25   24   26                                                       
CONECT   26   25   22   27                                                  
CONECT   27   26    1                                                       
CONECT   28   24   29   32                                                  
CONECT   29   28   30                                                       
CONECT   30   29   31                                                       
CONECT   31   30   32                                                       
CONECT   32   31   28                                                       
CONECT   33   23                                                            
CONECT   34    2                                                            
MASTER        0    0    0    0    0    0    0    0   34    0   78    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₇H₃₂O₇

Average Mass

468.5460 Da

Monoisotopic Mass

468.21480 Da

IUPAC Name

methyl 2-[(1R,2S,4R,6R,9R,10S,11R,15R,18R)-6-(furan-3-yl)-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

Traditional Name

methyl [(1R,2S,4R,6R,9R,10S,11R,15R,18R)-6-(furan-3-yl)-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

CAS Registry Number

Not Available

SMILES

COC(=O)C[C@H]1[C@@]2(C)[C@H](O[C@@H]3C[C@H](C(C)=C23)C2=COC=C2)[C@@H]2OC(=O)[C@]3(C)CCC(=O)[C@@]1(C)[C@@H]23

InChI Identifier

InChI=1S/C27H32O7/c1-13-15(14-7-9-32-12-14)10-16-20(13)27(4)17(11-19(29)31-5)26(3)18(28)6-8-25(2)22(26)21(23(27)33-16)34-24(25)30/h7,9,12,15-17,21-23H,6,8,10-11H2,1-5H3/t15-,16-,17-,21-,22+,23-,25-,26+,27-/m1/s1

InChI Key

IVORRUXZODBSHC-LSYMHUITSA-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, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, 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 excelsa	Plant	KNApSAcK

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
Dicarboxylic acid or derivatives
Gamma butyrolactone
Heteroaromatic compound
Methyl ester
Tetrahydrofuran
Furan
Carboxylic acid ester
Ketone
Lactone
Oxacycle
Carboxylic acid derivative
Organoheterocyclic compound
Dialkyl ether
Ether
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Organic oxide
Organic oxygen 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	3.67	ALOGPS
logP	3.15	ChemAxon
logS	-3.9	ALOGPS
pKa (Strongest Acidic)	18.85	ChemAxon
pKa (Strongest Basic)	-2.9	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	92.04 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	120.77 m³·mol⁻¹	ChemAxon
Polarizability	48.9 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

C00048939

Chemspider ID

8847329

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

10671977

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Lu XF, Lin PC, Zi JC, Fan XN: [Limonoids from seeds of Azadirachta indica and their antibacterial activity]. Zhongguo Zhong Yao Za Zhi. 2019 Nov;44(22):4864-4873. doi: 10.19540/j.cnki.cjcmm.20190813.202. [PubMed:31872594 ]
Chen J, Fan X, Zhu J, Song L, Li Z, Lin F, Yu R, Xu H, Zi J: Limonoids from seeds of Azadirachta indica A. Juss. and their cytotoxic activity. Acta Pharm Sin B. 2018 Jul;8(4):639-644. doi: 10.1016/j.apsb.2017.12.009. Epub 2018 Feb 1. [PubMed:30109187 ]

Showing NP-Card for (+)-2,3-Dihydronimbolide (NP0082142)

MOL for NP0082142 ((+)-2,3-Dihydronimbolide)

3D MOL for NP0082142 ((+)-2,3-Dihydronimbolide)

3D SDF for NP0082142 ((+)-2,3-Dihydronimbolide)

3D-SDF for NP0082142 ((+)-2,3-Dihydronimbolide)

PDB for NP0082142 ((+)-2,3-Dihydronimbolide)

3D PDB for NP0082142 ((+)-2,3-Dihydronimbolide)

SMILES for NP0082142 ((+)-2,3-Dihydronimbolide)

INCHI for NP0082142 ((+)-2,3-Dihydronimbolide)

Structure for NP0082142 ((+)-2,3-Dihydronimbolide)

3D Structure for NP0082142 ((+)-2,3-Dihydronimbolide)