NP-MRD: Showing NP-Card for (4r)-4-[(1s,3br,4r,5ar,9ar,9br,11as)-4-hydroxy-3b,6,6,9a,11a-pentamethyl-7-oxo-1h,2h,4h,5h,5ah,9bh,10h,11h-cyclopenta[a]phenanthren-1-yl]oxolan-2-one (NP0225989)

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Record Information

Version

2.0

Created at

2022-09-06 04:52:43 UTC

Updated at

2022-09-06 04:52:43 UTC

NP-MRD ID

NP0225989

Secondary Accession Numbers

None

Natural Product Identification

Common Name

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

Description

(13Alpha,17alpha)-7alpha-Hydroxy-4,4,8-trimethyl-3-oxo-5alpha-carda-1,14-dienolide 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. (4r)-4-[(1s,3br,4r,5ar,9ar,9br,11as)-4-hydroxy-3b,6,6,9a,11a-pentamethyl-7-oxo-1h,2h,4h,5h,5ah,9bh,10h,11h-cyclopenta[a]phenanthren-1-yl]oxolan-2-one is found in Xylocarpus moluccensis. Based on a literature review very few articles have been published on (13alpha,17alpha)-7alpha-Hydroxy-4,4,8-trimethyl-3-oxo-5alpha-carda-1,14-dienolide.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309062206522D          

 30 34  0  0  1  0            999 V2000
    1.8641    0.3651    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5776   -0.0491    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    2.3261   -1.4557    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1382   -1.6009    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6700   -0.9702    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
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    5.2655    0.9219    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0139   -0.4847    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
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M  END

     RDKit          3D

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M  END


  Mrv1652309062206522D          

 30 34  0  0  1  0            999 V2000
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M  END
> <DATABASE_ID>
NP0225989

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C26H36O4/c1-23(2)19-13-21(28)26(5)17-7-6-16(15-12-22(29)30-14-15)24(17,3)10-8-18(26)25(19,4)11-9-20(23)27/h7,9,11,15-16,18-19,21,28H,6,8,10,12-14H2,1-5H3/t15-,16-,18+,19-,21+,24-,25+,26-/m0/s1

> <INCHI_KEY>
FXSJHUUWDXXTPT-VHESCTIXSA-N

> <FORMULA>
C26H36O4

> <MOLECULAR_WEIGHT>
412.57

> <EXACT_MASS>
412.261359639

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
66

> <JCHEM_AVERAGE_POLARIZABILITY>
47.0289515893262

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(4R)-4-[(1R,2R,7R,9R,10R,14S,15S)-9-hydroxy-2,6,6,10,15-pentamethyl-5-oxotetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadeca-3,11-dien-14-yl]oxolan-2-one

> <JCHEM_LOGP>
3.8512293369999995

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-0.30377974020171006

> <JCHEM_POLAR_SURFACE_AREA>
63.6

> <JCHEM_REFRACTIVITY>
117.42109999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(4R)-4-[(1R,2R,7R,9R,10R,14S,15S)-9-hydroxy-2,6,6,10,15-pentamethyl-5-oxotetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadeca-3,11-dien-14-yl]oxolan-2-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 06-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-SEP-22         0                                  
HETATM    1  C   UNK     0       3.480   0.682   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.811  -0.092   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.342   1.354   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.819  -1.269   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       2.303  -0.998   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       4.342  -2.717   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       5.858  -2.988   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       6.851  -1.811   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       7.374  -3.259   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       6.327  -0.363   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       7.320   0.815   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       8.836   0.544   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       9.829   1.721   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       9.359  -0.905   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      10.352   0.273   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      10.875  -1.176   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      12.091  -0.231   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      13.366  -1.095   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      12.938  -2.574   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      13.883  -3.790   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      15.422  -3.740   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      15.945  -5.188   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0      14.730  -6.134   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0      14.780  -7.673   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0      13.455  -5.269   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      11.399  -2.624   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      12.070  -4.010   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      10.406  -3.802   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       8.890  -3.531   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       8.367  -2.082   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    4   10                                             
CONECT    3    2                                                            
CONECT    4    2    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   10   30                                             
CONECT    9    8                                                            
CONECT   10    8    2   11                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12   15   16   30                                             
CONECT   15   14                                                            
CONECT   16   14   17   26                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20   26                                                  
CONECT   20   19   21   25                                                  
CONECT   21   20   22                                                       
CONECT   22   21   23                                                       
CONECT   23   22   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23   20                                                       
CONECT   26   19   16   27   28                                             
CONECT   27   26                                                            
CONECT   28   26   29                                                       
CONECT   29   28   30                                                       
CONECT   30   29    8   14                                                  
MASTER        0    0    0    0    0    0    0    0   30    0   68    0
END

View in JSmol

Synonyms

Value	Source
(13a,17a)-7a-Hydroxy-4,4,8-trimethyl-3-oxo-5a-carda-1,14-dienolide	Generator
(13Α,17α)-7α-hydroxy-4,4,8-trimethyl-3-oxo-5α-carda-1,14-dienolide	Generator

Chemical Formula

C₂₆H₃₆O₄

Average Mass

412.5700 Da

Monoisotopic Mass

412.26136 Da

IUPAC Name

(4R)-4-[(1R,2R,7R,9R,10R,14S,15S)-9-hydroxy-2,6,6,10,15-pentamethyl-5-oxotetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadeca-3,11-dien-14-yl]oxolan-2-one

Traditional Name

(4R)-4-[(1R,2R,7R,9R,10R,14S,15S)-9-hydroxy-2,6,6,10,15-pentamethyl-5-oxotetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadeca-3,11-dien-14-yl]oxolan-2-one

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C26H36O4/c1-23(2)19-13-21(28)26(5)17-7-6-16(15-12-22(29)30-14-15)24(17,3)10-8-18(26)25(19,4)11-9-20(23)27/h7,9,11,15-16,18-19,21,28H,6,8,10,12-14H2,1-5H3/t15-,16-,18+,19-,21+,24-,25+,26-/m0/s1

InChI Key

FXSJHUUWDXXTPT-VHESCTIXSA-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
Xylocarpus moluccensis	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 lactone
3-oxo-delta-1-steroid
3-oxosteroid
Hydroxysteroid
3-oxo-5-alpha-steroid
7-hydroxysteroid
Oxosteroid
Delta-1-steroid
Steroid
Cyclohexenone
Gamma butyrolactone
Cyclic alcohol
Tetrahydrofuran
Cyclic ketone
Lactone
Ketone
Carboxylic acid ester
Secondary alcohol
Monocarboxylic acid or derivatives
Organoheterocyclic compound
Oxacycle
Carboxylic acid derivative
Organooxygen compound
Hydrocarbon derivative
Organic oxygen compound
Carbonyl group
Alcohol
Organic oxide
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	3.85	ChemAxon
pKa (Strongest Basic)	-0.3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	63.6 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	117.42 m³·mol⁻¹	ChemAxon
Polarizability	47.03 Å³	ChemAxon
Number of Rings	5	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

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

101515880

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (4r)-4-[(1s,3br,4r,5ar,9ar,9br,11as)-4-hydroxy-3b,6,6,9a,11a-pentamethyl-7-oxo-1h,2h,4h,5h,5ah,9bh,10h,11h-cyclopenta[a]phenanthren-1-yl]oxolan-2-one (NP0225989)

MOL for NP0225989 ((4r)-4-[(1s,3br,4r,5ar,9ar,9br,11as)-4-hydroxy-3b,6,6,9a,11a-pentamethyl-7-oxo-1h,2h,4h,5h,5ah,9bh,10h,11h-cyclopenta[a]phenanthren-1-yl]oxolan-2-one)

3D MOL for NP0225989 ((4r)-4-[(1s,3br,4r,5ar,9ar,9br,11as)-4-hydroxy-3b,6,6,9a,11a-pentamethyl-7-oxo-1h,2h,4h,5h,5ah,9bh,10h,11h-cyclopenta[a]phenanthren-1-yl]oxolan-2-one)

3D SDF for NP0225989 ((4r)-4-[(1s,3br,4r,5ar,9ar,9br,11as)-4-hydroxy-3b,6,6,9a,11a-pentamethyl-7-oxo-1h,2h,4h,5h,5ah,9bh,10h,11h-cyclopenta[a]phenanthren-1-yl]oxolan-2-one)

3D-SDF for NP0225989 ((4r)-4-[(1s,3br,4r,5ar,9ar,9br,11as)-4-hydroxy-3b,6,6,9a,11a-pentamethyl-7-oxo-1h,2h,4h,5h,5ah,9bh,10h,11h-cyclopenta[a]phenanthren-1-yl]oxolan-2-one)

PDB for NP0225989 ((4r)-4-[(1s,3br,4r,5ar,9ar,9br,11as)-4-hydroxy-3b,6,6,9a,11a-pentamethyl-7-oxo-1h,2h,4h,5h,5ah,9bh,10h,11h-cyclopenta[a]phenanthren-1-yl]oxolan-2-one)

3D PDB for NP0225989 ((4r)-4-[(1s,3br,4r,5ar,9ar,9br,11as)-4-hydroxy-3b,6,6,9a,11a-pentamethyl-7-oxo-1h,2h,4h,5h,5ah,9bh,10h,11h-cyclopenta[a]phenanthren-1-yl]oxolan-2-one)

SMILES for NP0225989 ((4r)-4-[(1s,3br,4r,5ar,9ar,9br,11as)-4-hydroxy-3b,6,6,9a,11a-pentamethyl-7-oxo-1h,2h,4h,5h,5ah,9bh,10h,11h-cyclopenta[a]phenanthren-1-yl]oxolan-2-one)

INCHI for NP0225989 ((4r)-4-[(1s,3br,4r,5ar,9ar,9br,11as)-4-hydroxy-3b,6,6,9a,11a-pentamethyl-7-oxo-1h,2h,4h,5h,5ah,9bh,10h,11h-cyclopenta[a]phenanthren-1-yl]oxolan-2-one)

Structure for NP0225989 ((4r)-4-[(1s,3br,4r,5ar,9ar,9br,11as)-4-hydroxy-3b,6,6,9a,11a-pentamethyl-7-oxo-1h,2h,4h,5h,5ah,9bh,10h,11h-cyclopenta[a]phenanthren-1-yl]oxolan-2-one)

3D Structure for NP0225989 ((4r)-4-[(1s,3br,4r,5ar,9ar,9br,11as)-4-hydroxy-3b,6,6,9a,11a-pentamethyl-7-oxo-1h,2h,4h,5h,5ah,9bh,10h,11h-cyclopenta[a]phenanthren-1-yl]oxolan-2-one)