NP-MRD: Showing NP-Card for limocin B (NP0084182)

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Record Information

Version

2.0

Created at

2022-04-29 04:59:27 UTC

Updated at

2022-04-29 04:59:27 UTC

NP-MRD ID

NP0084182

Secondary Accession Numbers

None

Natural Product Identification

Common Name

limocin B

Description

14-(5-Methoxyoxolan-3-yl)-2,6,6,10,15-pentamethyl-5-oxotetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]Heptadeca-3,11-dien-9-yl acetate 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. limocin B is found in Azadirachta indica . 14-(5-Methoxyoxolan-3-yl)-2,6,6,10,15-pentamethyl-5-oxotetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]Heptadeca-3,11-dien-9-yl acetate is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1533004231519392D          

 34 38  0  0  0  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1533004231519392D          

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 12 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 17 19  1  0  0  0  0
 19 20  2  0  0  0  0
 20 21  1  0  0  0  0
 21 22  2  0  0  0  0
 21 23  1  0  0  0  0
 23 24  1  0  0  0  0
 23 25  1  0  0  0  0
 23 26  1  0  0  0  0
 17 26  1  0  0  0  0
 26 27  1  0  0  0  0
 27 28  1  0  0  0  0
 28 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
 28 33  1  0  0  0  0
 11 33  1  0  0  0  0
 16 33  1  0  0  0  0
 33 34  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0084182

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1CC(CO1)C1CC=C2C1(C)CCC1C3(C)C=CC(=O)C(C)(C)C3CC(OC(C)=O)C21C

> <INCHI_IDENTIFIER>
InChI=1S/C29H42O5/c1-17(30)34-24-15-22-26(2,3)23(31)11-13-28(22,5)21-10-12-27(4)19(8-9-20(27)29(21,24)6)18-14-25(32-7)33-16-18/h9,11,13,18-19,21-22,24-25H,8,10,12,14-16H2,1-7H3

> <INCHI_KEY>
KLMZLZDZRFJUNS-UHFFFAOYSA-N

> <FORMULA>
C29H42O5

> <MOLECULAR_WEIGHT>
470.65

> <EXACT_MASS>
470.303224452

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
76

> <JCHEM_AVERAGE_POLARIZABILITY>
54.285951394047444

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
14-(5-methoxyoxolan-3-yl)-2,6,6,10,15-pentamethyl-5-oxotetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadeca-3,11-dien-9-yl acetate

> <ALOGPS_LOGP>
5.25

> <JCHEM_LOGP>
4.723351439333334

> <ALOGPS_LOGS>
-5.85

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-3.9681676225955234

> <JCHEM_POLAR_SURFACE_AREA>
61.830000000000005

> <JCHEM_REFRACTIVITY>
132.7095

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.70e-04 g/l

> <JCHEM_TRADITIONAL_IUPAC>
14-(5-methoxyoxolan-3-yl)-2,6,6,10,15-pentamethyl-5-oxotetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadeca-3,11-dien-9-yl acetate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 23-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-APR-15         0                                  
HETATM    1  C   UNK     0      -1.473   0.936   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0      -0.115   0.210   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0      -0.065  -1.329   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.209  -2.193   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.781  -3.673   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.758  -3.723   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      -1.281  -2.274   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       1.726  -4.889   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.298  -6.368   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.573  -7.232   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       3.789  -6.287   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       3.266  -4.839   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       2.594  -3.453   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.258  -3.661   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       5.774  -3.932   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       6.297  -5.381   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       7.813  -5.652   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       7.290  -4.203   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       8.806  -4.474   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      10.322  -4.746   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      10.845  -6.194   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      12.361  -6.465   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0       9.853  -7.371   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      11.184  -8.144   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       9.322  -8.817   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       8.337  -7.100   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       7.344  -8.277   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       5.828  -8.006   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0       4.835  -9.184   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0       5.358 -10.632   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0       6.874 -10.903   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0       4.366 -11.809   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       5.305  -6.558   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       4.312  -7.735   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    7                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6    8                                                  
CONECT    6    5    7                                                       
CONECT    7    6    3                                                       
CONECT    8    5    9   12                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   33                                                  
CONECT   12   11    8   13   14                                             
CONECT   13   12                                                            
CONECT   14   12   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17   33                                                  
CONECT   17   16   18   19   26                                             
CONECT   18   17                                                            
CONECT   19   17   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21   24   25   26                                             
CONECT   24   23                                                            
CONECT   25   23                                                            
CONECT   26   23   17   27                                                  
CONECT   27   26   28                                                       
CONECT   28   27   29   33                                                  
CONECT   29   28   30                                                       
CONECT   30   29   31   32                                                  
CONECT   31   30                                                            
CONECT   32   30                                                            
CONECT   33   28   11   16   34                                             
CONECT   34   33                                                            
MASTER        0    0    0    0    0    0    0    0   34    0   76    0
END

View in JSmol

Synonyms

Value	Source
14-(5-Methoxyoxolan-3-yl)-2,6,6,10,15-pentamethyl-5-oxotetracyclo[8.7.0.0,.0,]heptadeca-3,11-dien-9-yl acetic acid	Generator
14-(5-Methoxyoxolan-3-yl)-2,6,6,10,15-pentamethyl-5-oxotetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadeca-3,11-dien-9-yl acetic acid	Generator

Chemical Formula

C₂₉H₄₂O₅

Average Mass

470.6500 Da

Monoisotopic Mass

470.30322 Da

IUPAC Name

14-(5-methoxyoxolan-3-yl)-2,6,6,10,15-pentamethyl-5-oxotetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadeca-3,11-dien-9-yl acetate

Traditional Name

14-(5-methoxyoxolan-3-yl)-2,6,6,10,15-pentamethyl-5-oxotetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadeca-3,11-dien-9-yl acetate

CAS Registry Number

Not Available

SMILES

COC1CC(CO1)C1CC=C2C1(C)CCC1C3(C)C=CC(=O)C(C)(C)C3CC(OC(C)=O)C21C

InChI Identifier

InChI=1S/C29H42O5/c1-17(30)34-24-15-22-26(2,3)23(31)11-13-28(22,5)21-10-12-27(4)19(8-9-20(27)29(21,24)6)18-14-25(32-7)33-16-18/h9,11,13,18-19,21-22,24-25H,8,10,12,14-16H2,1-7H3

InChI Key

KLMZLZDZRFJUNS-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, 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 indica	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
Steroid ester
3-oxo-delta-1-steroid
3-oxosteroid
Oxosteroid
Delta-1-steroid
Steroid
Cyclohexenone
Tetrahydrofuran
Carboxylic acid ester
Ketone
Cyclic ketone
Acetal
Carboxylic acid derivative
Oxacycle
Organoheterocyclic compound
Monocarboxylic acid or derivatives
Organic oxide
Hydrocarbon derivative
Organic oxygen compound
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	5.25	ALOGPS
logP	4.72	ChemAxon
logS	-5.8	ALOGPS
pKa (Strongest Basic)	-4	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	61.83 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	132.71 m³·mol⁻¹	ChemAxon
Polarizability	54.29 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	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

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for limocin B (NP0084182)

MOL for NP0084182 (limocin B)

3D MOL for NP0084182 (limocin B)

3D SDF for NP0084182 (limocin B)

3D-SDF for NP0084182 (limocin B)

PDB for NP0084182 (limocin B)

3D PDB for NP0084182 (limocin B)

SMILES for NP0084182 (limocin B)

INCHI for NP0084182 (limocin B)

Structure for NP0084182 (limocin B)

3D Structure for NP0084182 (limocin B)