NP-MRD: Showing NP-Card for (1s,3br,4r,5ar,9ar,9br,11as)-1-[(3s)-5-methoxyoxolan-3-yl]-3b,6,6,9a,11a-pentamethyl-7-oxo-1h,2h,4h,5h,5ah,9bh,10h,11h-cyclopenta[a]phenanthren-4-yl acetate (NP0184587)

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Record Information

Version

2.0

Created at

2022-09-03 23:44:58 UTC

Updated at

2022-09-03 23:44:58 UTC

NP-MRD ID

NP0184587

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1s,3br,4r,5ar,9ar,9br,11as)-1-[(3s)-5-methoxyoxolan-3-yl]-3b,6,6,9a,11a-pentamethyl-7-oxo-1h,2h,4h,5h,5ah,9bh,10h,11h-cyclopenta[a]phenanthren-4-yl acetate

Description

Limocin B 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,3br,4r,5ar,9ar,9br,11as)-1-[(3s)-5-methoxyoxolan-3-yl]-3b,6,6,9a,11a-pentamethyl-7-oxo-1h,2h,4h,5h,5ah,9bh,10h,11h-cyclopenta[a]phenanthren-4-yl acetate is found in Azadirachta indica. Based on a literature review very few articles have been published on Limocin B.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309042201442D          

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M  END

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M  END


  Mrv1652309042201442D          

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  6  7  1  1  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
  6 10  1  0  0  0  0
 10 11  1  1  0  0  0
 10 12  1  0  0  0  0
 12 13  1  0  0  0  0
 14 13  1  6  0  0  0
 14 15  1  0  0  0  0
 15 16  1  6  0  0  0
 15 17  1  0  0  0  0
 17 18  2  0  0  0  0
 18 19  1  0  0  0  0
 19 20  2  0  0  0  0
 19 21  1  0  0  0  0
 21 22  1  0  0  0  0
 21 23  1  0  0  0  0
 21 24  1  0  0  0  0
 15 24  1  0  0  0  0
 24 25  1  6  0  0  0
 25 26  1  0  0  0  0
 26 27  1  1  0  0  0
 27 28  1  0  0  0  0
 28 29  1  0  0  0  0
 28 30  2  0  0  0  0
 26 31  1  0  0  0  0
  9 31  1  0  0  0  0
 14 31  1  0  0  0  0
 31 32  1  6  0  0  0
  5 33  1  0  0  0  0
 33 34  1  0  0  0  0
  3 34  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0184587

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1C[C@H](CO1)[C@@H]1CC=C2[C@@]1(C)CC[C@@H]1[C@@]3(C)C=CC(=O)C(C)(C)[C@@H]3C[C@@H](OC(C)=O)[C@@]21C

> <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/t18-,19+,21-,22+,24-,25?,27+,28-,29+/m1/s1

> <INCHI_KEY>
KLMZLZDZRFJUNS-LUWOXTEUSA-N

> <FORMULA>
C29H42O5

> <MOLECULAR_WEIGHT>
470.65

> <EXACT_MASS>
470.303224452

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
76

> <JCHEM_AVERAGE_POLARIZABILITY>
53.854870323142485

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1R,2R,7R,9R,10R,14S,15S)-14-[(3S)-5-methoxyoxolan-3-yl]-2,6,6,10,15-pentamethyl-5-oxotetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadeca-3,11-dien-9-yl acetate

> <JCHEM_LOGP>
4.723351439333334

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-3.9681676225955234

> <JCHEM_POLAR_SURFACE_AREA>
61.83

> <JCHEM_REFRACTIVITY>
132.7095

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1R,2R,7R,9R,10R,14S,15S)-14-[(3S)-5-methoxyoxolan-3-yl]-2,6,6,10,15-pentamethyl-5-oxotetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadeca-3,11-dien-9-yl acetate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 04-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-22         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       1.726  -4.889   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.298  -6.368   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.573  -7.232   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.789  -6.287   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       3.266  -4.839   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.594  -3.453   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.258  -3.661   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.774  -3.932   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       6.297  -5.381   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       7.813  -5.652   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       7.290  -4.203   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       8.806  -4.474   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      10.322  -4.746   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      10.845  -6.194   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      12.361  -6.465   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       9.853  -7.371   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      11.184  -8.144   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       9.322  -8.817   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       8.337  -7.100   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       7.344  -8.277   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       5.828  -8.006   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0       4.835  -9.184   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0       5.358 -10.632   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       6.874 -10.903   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0       4.366 -11.809   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0       5.305  -6.558   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       4.312  -7.735   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      -0.758  -3.723   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0      -1.281  -2.274   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   34                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   33                                                  
CONECT    6    5    7   10                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   31                                                  
CONECT   10    9    6   11   12                                             
CONECT   11   10                                                            
CONECT   12   10   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15   31                                                  
CONECT   15   14   16   17   24                                             
CONECT   16   15                                                            
CONECT   17   15   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19   22   23   24                                             
CONECT   22   21                                                            
CONECT   23   21                                                            
CONECT   24   21   15   25                                                  
CONECT   25   24   26                                                       
CONECT   26   25   27   31                                                  
CONECT   27   26   28                                                       
CONECT   28   27   29   30                                                  
CONECT   29   28                                                            
CONECT   30   28                                                            
CONECT   31   26    9   14   32                                             
CONECT   32   31                                                            
CONECT   33    5   34                                                       
CONECT   34   33    3                                                       
MASTER        0    0    0    0    0    0    0    0   34    0   76    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₉H₄₂O₅

Average Mass

470.6500 Da

Monoisotopic Mass

470.30322 Da

IUPAC Name

(1R,2R,7R,9R,10R,14S,15S)-14-[(3S)-5-methoxyoxolan-3-yl]-2,6,6,10,15-pentamethyl-5-oxotetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadeca-3,11-dien-9-yl acetate

Traditional Name

(1R,2R,7R,9R,10R,14S,15S)-14-[(3S)-5-methoxyoxolan-3-yl]-2,6,6,10,15-pentamethyl-5-oxotetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadeca-3,11-dien-9-yl acetate

CAS Registry Number

Not Available

SMILES

COC1C[C@H](CO1)[C@@H]1CC=C2[C@@]1(C)CC[C@@H]1[C@@]3(C)C=CC(=O)C(C)(C)[C@@H]3C[C@@H](OC(C)=O)[C@@]21C

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/t18-,19+,21-,22+,24-,25?,27+,28-,29+/m1/s1

InChI Key

KLMZLZDZRFJUNS-LUWOXTEUSA-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
Steroid ester
3-oxo-5-alpha-steroid
Oxosteroid
3-oxosteroid
3-oxo-delta-1-steroid
Steroid
Delta-1-steroid
Cyclohexenone
Tetrahydrofuran
Cyclic ketone
Ketone
Carboxylic acid ester
Oxacycle
Organoheterocyclic compound
Monocarboxylic acid or derivatives
Carboxylic acid derivative
Acetal
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
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	4.72	ChemAxon
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	53.85 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

C00052615

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

101602321

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (1s,3br,4r,5ar,9ar,9br,11as)-1-[(3s)-5-methoxyoxolan-3-yl]-3b,6,6,9a,11a-pentamethyl-7-oxo-1h,2h,4h,5h,5ah,9bh,10h,11h-cyclopenta[a]phenanthren-4-yl acetate (NP0184587)

MOL for NP0184587 ((1s,3br,4r,5ar,9ar,9br,11as)-1-[(3s)-5-methoxyoxolan-3-yl]-3b,6,6,9a,11a-pentamethyl-7-oxo-1h,2h,4h,5h,5ah,9bh,10h,11h-cyclopenta[a]phenanthren-4-yl acetate)

3D MOL for NP0184587 ((1s,3br,4r,5ar,9ar,9br,11as)-1-[(3s)-5-methoxyoxolan-3-yl]-3b,6,6,9a,11a-pentamethyl-7-oxo-1h,2h,4h,5h,5ah,9bh,10h,11h-cyclopenta[a]phenanthren-4-yl acetate)

3D SDF for NP0184587 ((1s,3br,4r,5ar,9ar,9br,11as)-1-[(3s)-5-methoxyoxolan-3-yl]-3b,6,6,9a,11a-pentamethyl-7-oxo-1h,2h,4h,5h,5ah,9bh,10h,11h-cyclopenta[a]phenanthren-4-yl acetate)

3D-SDF for NP0184587 ((1s,3br,4r,5ar,9ar,9br,11as)-1-[(3s)-5-methoxyoxolan-3-yl]-3b,6,6,9a,11a-pentamethyl-7-oxo-1h,2h,4h,5h,5ah,9bh,10h,11h-cyclopenta[a]phenanthren-4-yl acetate)

PDB for NP0184587 ((1s,3br,4r,5ar,9ar,9br,11as)-1-[(3s)-5-methoxyoxolan-3-yl]-3b,6,6,9a,11a-pentamethyl-7-oxo-1h,2h,4h,5h,5ah,9bh,10h,11h-cyclopenta[a]phenanthren-4-yl acetate)

3D PDB for NP0184587 ((1s,3br,4r,5ar,9ar,9br,11as)-1-[(3s)-5-methoxyoxolan-3-yl]-3b,6,6,9a,11a-pentamethyl-7-oxo-1h,2h,4h,5h,5ah,9bh,10h,11h-cyclopenta[a]phenanthren-4-yl acetate)

SMILES for NP0184587 ((1s,3br,4r,5ar,9ar,9br,11as)-1-[(3s)-5-methoxyoxolan-3-yl]-3b,6,6,9a,11a-pentamethyl-7-oxo-1h,2h,4h,5h,5ah,9bh,10h,11h-cyclopenta[a]phenanthren-4-yl acetate)

INCHI for NP0184587 ((1s,3br,4r,5ar,9ar,9br,11as)-1-[(3s)-5-methoxyoxolan-3-yl]-3b,6,6,9a,11a-pentamethyl-7-oxo-1h,2h,4h,5h,5ah,9bh,10h,11h-cyclopenta[a]phenanthren-4-yl acetate)

Structure for NP0184587 ((1s,3br,4r,5ar,9ar,9br,11as)-1-[(3s)-5-methoxyoxolan-3-yl]-3b,6,6,9a,11a-pentamethyl-7-oxo-1h,2h,4h,5h,5ah,9bh,10h,11h-cyclopenta[a]phenanthren-4-yl acetate)

3D Structure for NP0184587 ((1s,3br,4r,5ar,9ar,9br,11as)-1-[(3s)-5-methoxyoxolan-3-yl]-3b,6,6,9a,11a-pentamethyl-7-oxo-1h,2h,4h,5h,5ah,9bh,10h,11h-cyclopenta[a]phenanthren-4-yl acetate)