NP-MRD: Showing NP-Card for (1r,2r,4s,7r,8s,11r,12r,13s,16r)-13-hydroxy-7-(5-hydroxy-2-oxo-5h-furan-3-yl)-1,8,12,13,15,15-hexamethyl-3,6,14-trioxapentacyclo[9.7.0.0²,⁴.0²,⁸.0¹²,¹⁶]octadecane-5,18-dione (NP0231936)

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Record Information

Version

2.0

Created at

2022-09-06 12:59:57 UTC

Updated at

2022-09-06 12:59:57 UTC

NP-MRD ID

NP0231936

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1r,2r,4s,7r,8s,11r,12r,13s,16r)-13-hydroxy-7-(5-hydroxy-2-oxo-5h-furan-3-yl)-1,8,12,13,15,15-hexamethyl-3,6,14-trioxapentacyclo[9.7.0.0²,⁴.0²,⁸.0¹²,¹⁶]octadecane-5,18-dione

Description

Sudachinoid B belongs to the class of organic compounds known as steroid lactones. These are sterol lipids containing a lactone moiety linked to the steroid skeleton. (1r,2r,4s,7r,8s,11r,12r,13s,16r)-13-hydroxy-7-(5-hydroxy-2-oxo-5h-furan-3-yl)-1,8,12,13,15,15-hexamethyl-3,6,14-trioxapentacyclo[9.7.0.0²,⁴.0²,⁸.0¹²,¹⁶]octadecane-5,18-dione is found in Citrus medica. (1r,2r,4s,7r,8s,11r,12r,13s,16r)-13-hydroxy-7-(5-hydroxy-2-oxo-5h-furan-3-yl)-1,8,12,13,15,15-hexamethyl-3,6,14-trioxapentacyclo[9.7.0.0²,⁴.0²,⁸.0¹²,¹⁶]octadecane-5,18-dione was first documented in 2020 (PMID: 32971925). Based on a literature review very few articles have been published on Sudachinoid B.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309062214592D          

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M  END

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M  END


  Mrv1652309062214592D          

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 32 33  1  1  0  0  0
 34 33  1  1  0  0  0
 32 34  1  0  0  0  0
 19 34  1  0  0  0  0
 14 34  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0231936

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC1(C)O[C@](C)(O)[C@@]2(C)[C@H]1CC(=O)[C@]1(C)[C@@H]2CC[C@@]2(C)[C@@H](OC(=O)[C@H]3O[C@@]123)C1=CC(O)OC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C25H32O9/c1-20(2)13-10-14(26)23(5)12(22(13,4)24(6,30)34-20)7-8-21(3)16(11-9-15(27)31-18(11)28)32-19(29)17-25(21,23)33-17/h9,12-13,15-17,27,30H,7-8,10H2,1-6H3/t12-,13+,15?,16+,17-,21+,22-,23+,24+,25-/m1/s1

> <INCHI_KEY>
NABBIRQIEXBJDL-TUXRQYSISA-N

> <FORMULA>
C25H32O9

> <MOLECULAR_WEIGHT>
476.522

> <EXACT_MASS>
476.20463261

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
66

> <JCHEM_AVERAGE_POLARIZABILITY>
48.10703845846584

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1R,2R,4S,7R,8S,11R,12R,13S,16R)-13-hydroxy-7-(5-hydroxy-2-oxo-2,5-dihydrofuran-3-yl)-1,8,12,13,15,15-hexamethyl-3,6,14-trioxapentacyclo[9.7.0.0^{2,4}.0^{2,8}.0^{12,16}]octadecane-5,18-dione

> <JCHEM_LOGP>
2.1235962529999997

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.112177406593709

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.508108304811369

> <JCHEM_PKA_STRONGEST_BASIC>
-4.042867420282225

> <JCHEM_POLAR_SURFACE_AREA>
131.89000000000001

> <JCHEM_REFRACTIVITY>
115.05599999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1R,2R,4S,7R,8S,11R,12R,13S,16R)-13-hydroxy-7-(5-hydroxy-2-oxo-5H-furan-3-yl)-1,8,12,13,15,15-hexamethyl-3,6,14-trioxapentacyclo[9.7.0.0^{2,4}.0^{2,8}.0^{12,16}]octadecane-5,18-dione

> <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      10.453   2.075   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       8.937   1.804   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       8.826   3.340   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       9.365   0.325   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       8.090  -0.539   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       9.083  -1.717   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       7.023  -1.650   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       6.874   0.406   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       6.505  -1.089   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       7.398   1.854   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       6.405   3.032   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.889   2.761   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       3.896   3.938   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       4.366   1.312   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       4.254   2.848   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       5.358   0.135   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       4.835  -1.314   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       3.319  -1.585   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       2.326  -0.407   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       1.803  -1.856   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       0.810  -0.678   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       0.287  -2.127   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       1.151  -3.401   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       0.206  -4.617   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0       0.634  -6.097   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0      -1.242  -4.094   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0      -1.192  -2.555   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0      -2.408  -1.610   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0      -0.182   0.499   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0       0.341   1.947   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0      -0.652   3.125   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0       1.857   2.218   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0       3.373   2.489   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0       2.850   1.041   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    4   10                                             
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6    7    8                                             
CONECT    6    5                                                            
CONECT    7    5                                                            
CONECT    8    5    9   10   16                                             
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   34                                             
CONECT   15   14                                                            
CONECT   16   14    8   17                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20   21   34                                             
CONECT   20   19                                                            
CONECT   21   19   22   29                                                  
CONECT   22   21   23   27                                                  
CONECT   23   22   24                                                       
CONECT   24   23   25   26                                                  
CONECT   25   24                                                            
CONECT   26   24   27                                                       
CONECT   27   26   22   28                                                  
CONECT   28   27                                                            
CONECT   29   21   30                                                       
CONECT   30   29   31   32                                                  
CONECT   31   30                                                            
CONECT   32   30   33   34                                                  
CONECT   33   32   34                                                       
CONECT   34   33   32   19   14                                             
MASTER        0    0    0    0    0    0    0    0   34    0   78    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₅H₃₂O₉

Average Mass

476.5220 Da

Monoisotopic Mass

476.20463 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

CC1(C)O[C@](C)(O)[C@@]2(C)[C@H]1CC(=O)[C@]1(C)[C@@H]2CC[C@@]2(C)[C@@H](OC(=O)[C@H]3O[C@@]123)C1=CC(O)OC1=O

InChI Identifier

InChI=1S/C25H32O9/c1-20(2)13-10-14(26)23(5)12(22(13,4)24(6,30)34-20)7-8-21(3)16(11-9-15(27)31-18(11)28)32-19(29)17-25(21,23)33-17/h9,12-13,15-17,27,30H,7-8,10H2,1-6H3/t12-,13+,15?,16+,17-,21+,22-,23+,24+,25-/m1/s1

InChI Key

NABBIRQIEXBJDL-TUXRQYSISA-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
Citrus medica	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as steroid lactones. These are sterol lipids containing a lactone moiety linked to the steroid skeleton.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Steroids and steroid derivatives

Sub Class

Steroid lactones

Direct Parent

Steroid lactones

Alternative Parents

Substituents

Steroid lactone
15-hydroxysteroid
Hydroxysteroid
2-oxosteroid
Oxosteroid
11-oxosteroid
Naphthopyran
Naphthalene
1,4-dioxepane
Delta valerolactone
Dioxepane
Delta_valerolactone
2-furanone
Dicarboxylic acid or derivatives
Pyran
Oxane
Dihydrofuran
Alpha,beta-unsaturated carboxylic ester
Enoate ester
Oxolane
Hemiacetal
Carboxylic acid ester
Ketone
Lactone
Ether
Oxirane
Organoheterocyclic compound
Oxacycle
Dialkyl ether
Carboxylic acid derivative
Organic oxide
Organic oxygen compound
Hydrocarbon derivative
Carbonyl group
Organooxygen compound
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

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00033394

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

101718896

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Shin J, Song HY, Lee M: Sudachinoid- and Ichangensin-Type Limonoids from Citrus junos Downregulate Pro-Inflammatory Cytokines. Int J Mol Sci. 2020 Sep 22;21(18):6963. doi: 10.3390/ijms21186963. [PubMed:32971925 ]
LOTUS database [Link]

Showing NP-Card for (1r,2r,4s,7r,8s,11r,12r,13s,16r)-13-hydroxy-7-(5-hydroxy-2-oxo-5h-furan-3-yl)-1,8,12,13,15,15-hexamethyl-3,6,14-trioxapentacyclo[9.7.0.0²,⁴.0²,⁸.0¹²,¹⁶]octadecane-5,18-dione (NP0231936)

MOL for NP0231936 ((1r,2r,4s,7r,8s,11r,12r,13s,16r)-13-hydroxy-7-(5-hydroxy-2-oxo-5h-furan-3-yl)-1,8,12,13,15,15-hexamethyl-3,6,14-trioxapentacyclo[9.7.0.0²,⁴.0²,⁸.0¹²,¹⁶]octadecane-5,18-dione)

3D MOL for NP0231936 ((1r,2r,4s,7r,8s,11r,12r,13s,16r)-13-hydroxy-7-(5-hydroxy-2-oxo-5h-furan-3-yl)-1,8,12,13,15,15-hexamethyl-3,6,14-trioxapentacyclo[9.7.0.0²,⁴.0²,⁸.0¹²,¹⁶]octadecane-5,18-dione)

3D SDF for NP0231936 ((1r,2r,4s,7r,8s,11r,12r,13s,16r)-13-hydroxy-7-(5-hydroxy-2-oxo-5h-furan-3-yl)-1,8,12,13,15,15-hexamethyl-3,6,14-trioxapentacyclo[9.7.0.0²,⁴.0²,⁸.0¹²,¹⁶]octadecane-5,18-dione)

3D-SDF for NP0231936 ((1r,2r,4s,7r,8s,11r,12r,13s,16r)-13-hydroxy-7-(5-hydroxy-2-oxo-5h-furan-3-yl)-1,8,12,13,15,15-hexamethyl-3,6,14-trioxapentacyclo[9.7.0.0²,⁴.0²,⁸.0¹²,¹⁶]octadecane-5,18-dione)

PDB for NP0231936 ((1r,2r,4s,7r,8s,11r,12r,13s,16r)-13-hydroxy-7-(5-hydroxy-2-oxo-5h-furan-3-yl)-1,8,12,13,15,15-hexamethyl-3,6,14-trioxapentacyclo[9.7.0.0²,⁴.0²,⁸.0¹²,¹⁶]octadecane-5,18-dione)

3D PDB for NP0231936 ((1r,2r,4s,7r,8s,11r,12r,13s,16r)-13-hydroxy-7-(5-hydroxy-2-oxo-5h-furan-3-yl)-1,8,12,13,15,15-hexamethyl-3,6,14-trioxapentacyclo[9.7.0.0²,⁴.0²,⁸.0¹²,¹⁶]octadecane-5,18-dione)

SMILES for NP0231936 ((1r,2r,4s,7r,8s,11r,12r,13s,16r)-13-hydroxy-7-(5-hydroxy-2-oxo-5h-furan-3-yl)-1,8,12,13,15,15-hexamethyl-3,6,14-trioxapentacyclo[9.7.0.0²,⁴.0²,⁸.0¹²,¹⁶]octadecane-5,18-dione)

INCHI for NP0231936 ((1r,2r,4s,7r,8s,11r,12r,13s,16r)-13-hydroxy-7-(5-hydroxy-2-oxo-5h-furan-3-yl)-1,8,12,13,15,15-hexamethyl-3,6,14-trioxapentacyclo[9.7.0.0²,⁴.0²,⁸.0¹²,¹⁶]octadecane-5,18-dione)

Structure for NP0231936 ((1r,2r,4s,7r,8s,11r,12r,13s,16r)-13-hydroxy-7-(5-hydroxy-2-oxo-5h-furan-3-yl)-1,8,12,13,15,15-hexamethyl-3,6,14-trioxapentacyclo[9.7.0.0²,⁴.0²,⁸.0¹²,¹⁶]octadecane-5,18-dione)

3D Structure for NP0231936 ((1r,2r,4s,7r,8s,11r,12r,13s,16r)-13-hydroxy-7-(5-hydroxy-2-oxo-5h-furan-3-yl)-1,8,12,13,15,15-hexamethyl-3,6,14-trioxapentacyclo[9.7.0.0²,⁴.0²,⁸.0¹²,¹⁶]octadecane-5,18-dione)