NP-MRD: Showing NP-Card for (1r,2r,4s,7r,8s,11r,12r,13s,16r)-7-(5-hydroxy-2-oxo-5h-furan-3-yl)-13-methoxy-1,8,12,13,15,15-hexamethyl-3,6,14-trioxapentacyclo[9.7.0.0²,⁴.0²,⁸.0¹²,¹⁶]octadecane-5,18-dione (NP0280949)

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Record Information

Version

2.0

Created at

2022-09-09 07:00:55 UTC

Updated at

2022-09-09 07:00:55 UTC

NP-MRD ID

NP0280949

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1r,2r,4s,7r,8s,11r,12r,13s,16r)-7-(5-hydroxy-2-oxo-5h-furan-3-yl)-13-methoxy-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 A 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)-7-(5-hydroxy-2-oxo-5h-furan-3-yl)-13-methoxy-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 sudachi. (1r,2r,4s,7r,8s,11r,12r,13s,16r)-7-(5-hydroxy-2-oxo-5h-furan-3-yl)-13-methoxy-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 2016 (PMID: 28901103). Based on a literature review very few articles have been published on Sudachinoid A (PMID: 32971925).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309092209002D          

 35 40  0  0  1  0            999 V2000
    5.6779   -0.7744    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    4.7280    1.7894    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END

     RDKit          3D

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M  END


  Mrv1652309092209002D          

 35 40  0  0  1  0            999 V2000
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 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  6  0  0  0
 18 20  1  0  0  0  0
 20 21  1  6  0  0  0
 21 22  2  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 23 25  1  0  0  0  0
 25 26  1  0  0  0  0
 21 26  1  0  0  0  0
 26 27  2  0  0  0  0
 20 28  1  0  0  0  0
 28 29  1  0  0  0  0
 29 30  2  0  0  0  0
 29 31  1  0  0  0  0
 31 32  1  1  0  0  0
 33 32  1  1  0  0  0
 31 33  1  0  0  0  0
 18 33  1  0  0  0  0
 13 33  1  0  0  0  0
 15 34  1  0  0  0  0
  9 34  1  0  0  0  0
  3 34  1  0  0  0  0
 34 35  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0280949

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CO[C@@]1(C)OC(C)(C)[C@@H]2CC(=O)[C@]3(C)[C@H](CC[C@@]4(C)[C@@H](OC(=O)[C@H]5O[C@@]345)C3=CC(O)OC3=O)[C@@]12C

> <INCHI_IDENTIFIER>
InChI=1S/C26H34O9/c1-21(2)14-11-15(27)24(5)13(23(14,4)25(6,31-7)35-21)8-9-22(3)17(12-10-16(28)32-19(12)29)33-20(30)18-26(22,24)34-18/h10,13-14,16-18,28H,8-9,11H2,1-7H3/t13-,14+,16?,17+,18-,22+,23-,24+,25+,26-/m1/s1

> <INCHI_KEY>
ZVOFIGKRVQYENS-XRAPKWHDSA-N

> <FORMULA>
C26H34O9

> <MOLECULAR_WEIGHT>
490.549

> <EXACT_MASS>
490.220282675

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
69

> <JCHEM_AVERAGE_POLARIZABILITY>
50.119019543175284

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1R,2R,4S,7R,8S,11R,12R,13S,16R)-7-(5-hydroxy-2-oxo-2,5-dihydrofuran-3-yl)-13-methoxy-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>
2.766722756666665

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.355290529257733

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.779694410163266

> <JCHEM_PKA_STRONGEST_BASIC>
-3.857618353960882

> <JCHEM_POLAR_SURFACE_AREA>
120.89000000000001

> <JCHEM_REFRACTIVITY>
119.80719999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1R,2R,4S,7R,8S,11R,12R,13S,16R)-7-(5-hydroxy-2-oxo-5H-furan-3-yl)-13-methoxy-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                                 09-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   09-SEP-22         0                                  
HETATM    1  C   UNK     0      10.599  -1.446   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       9.083  -1.717   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       8.090  -0.539   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       7.023  -1.650   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       9.365   0.325   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       8.937   1.804   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      10.453   2.075   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       8.826   3.340   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       7.398   1.854   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       6.405   3.032   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.889   2.761   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       3.896   3.938   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       4.366   1.312   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.254   2.848   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       5.358   0.135   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       4.835  -1.314   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       3.319  -1.585   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       2.326  -0.407   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       1.803  -1.856   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       0.810  -0.678   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       0.287  -2.127   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       1.151  -3.401   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       0.206  -4.617   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       0.634  -6.097   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0      -1.242  -4.094   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0      -1.192  -2.555   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0      -2.408  -1.610   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0      -0.182   0.499   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0       0.341   1.947   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0      -0.652   3.125   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0       1.857   2.218   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0       3.373   2.489   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0       2.850   1.041   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       6.874   0.406   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       6.505  -1.089   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    5   34                                             
CONECT    4    3                                                            
CONECT    5    3    6                                                       
CONECT    6    5    7    8    9                                             
CONECT    7    6                                                            
CONECT    8    6                                                            
CONECT    9    6   10   34                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14   15   33                                             
CONECT   14   13                                                            
CONECT   15   13   16   34                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19   20   33                                             
CONECT   19   18                                                            
CONECT   20   18   21   28                                                  
CONECT   21   20   22   26                                                  
CONECT   22   21   23                                                       
CONECT   23   22   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23   26                                                       
CONECT   26   25   21   27                                                  
CONECT   27   26                                                            
CONECT   28   20   29                                                       
CONECT   29   28   30   31                                                  
CONECT   30   29                                                            
CONECT   31   29   32   33                                                  
CONECT   32   31   33                                                       
CONECT   33   32   31   18   13                                             
CONECT   34   15    9    3   35                                             
CONECT   35   34                                                            
MASTER        0    0    0    0    0    0    0    0   35    0   80    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₆H₃₄O₉

Average Mass

490.5490 Da

Monoisotopic Mass

490.22028 Da

IUPAC Name

(1R,2R,4S,7R,8S,11R,12R,13S,16R)-7-(5-hydroxy-2-oxo-2,5-dihydrofuran-3-yl)-13-methoxy-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

Traditional Name

(1R,2R,4S,7R,8S,11R,12R,13S,16R)-7-(5-hydroxy-2-oxo-5H-furan-3-yl)-13-methoxy-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

CAS Registry Number

Not Available

SMILES

CO[C@@]1(C)OC(C)(C)[C@@H]2CC(=O)[C@]3(C)[C@H](CC[C@@]4(C)[C@@H](OC(=O)[C@H]5O[C@@]345)C3=CC(O)OC3=O)[C@@]12C

InChI Identifier

InChI=1S/C26H34O9/c1-21(2)14-11-15(27)24(5)13(23(14,4)25(6,31-7)35-21)8-9-22(3)17(12-10-16(28)32-19(12)29)33-20(30)18-26(22,24)34-18/h10,13-14,16-18,28H,8-9,11H2,1-7H3/t13-,14+,16?,17+,18-,22+,23-,24+,25+,26-/m1/s1

InChI Key

ZVOFIGKRVQYENS-XRAPKWHDSA-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 sudachi	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
11-oxosteroid
Oxosteroid
2-oxosteroid
Naphthopyran
Naphthalene
1,4-dioxepane
Ketal
Delta_valerolactone
Delta valerolactone
Dioxepane
2-furanone
Dicarboxylic acid or derivatives
Oxane
Pyran
Dihydrofuran
Oxolane
Enoate ester
Alpha,beta-unsaturated carboxylic ester
Carboxylic acid ester
Hemiacetal
Ketone
Lactone
Oxirane
Organoheterocyclic compound
Oxacycle
Dialkyl ether
Carboxylic acid derivative
Ether
Acetal
Organooxygen compound
Hydrocarbon derivative
Organic oxygen compound
Carbonyl group
Organic oxide
Aldehyde
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	2.77	ChemAxon
pKa (Strongest Acidic)	11.78	ChemAxon
pKa (Strongest Basic)	-3.9	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	120.89 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	119.81 m³·mol⁻¹	ChemAxon
Polarizability	50.12 Å³	ChemAxon
Number of Rings	6	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

C00033393

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

101718895

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 ]
Cheung TK, Li W, Ho HM, Liang ZT, Huang CQ: [Chemical variation in Aurantii Fructus before and after processing based on UHPLC-Q-TOF-MS]. Zhongguo Zhong Yao Za Zhi. 2016 Jun;41(11):2070-2080. doi: 10.4268/cjcmm20161116. [PubMed:28901103 ]
LOTUS database [Link]

Showing NP-Card for (1r,2r,4s,7r,8s,11r,12r,13s,16r)-7-(5-hydroxy-2-oxo-5h-furan-3-yl)-13-methoxy-1,8,12,13,15,15-hexamethyl-3,6,14-trioxapentacyclo[9.7.0.0²,⁴.0²,⁸.0¹²,¹⁶]octadecane-5,18-dione (NP0280949)

MOL for NP0280949 ((1r,2r,4s,7r,8s,11r,12r,13s,16r)-7-(5-hydroxy-2-oxo-5h-furan-3-yl)-13-methoxy-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 NP0280949 ((1r,2r,4s,7r,8s,11r,12r,13s,16r)-7-(5-hydroxy-2-oxo-5h-furan-3-yl)-13-methoxy-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 NP0280949 ((1r,2r,4s,7r,8s,11r,12r,13s,16r)-7-(5-hydroxy-2-oxo-5h-furan-3-yl)-13-methoxy-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 NP0280949 ((1r,2r,4s,7r,8s,11r,12r,13s,16r)-7-(5-hydroxy-2-oxo-5h-furan-3-yl)-13-methoxy-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 NP0280949 ((1r,2r,4s,7r,8s,11r,12r,13s,16r)-7-(5-hydroxy-2-oxo-5h-furan-3-yl)-13-methoxy-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 NP0280949 ((1r,2r,4s,7r,8s,11r,12r,13s,16r)-7-(5-hydroxy-2-oxo-5h-furan-3-yl)-13-methoxy-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 NP0280949 ((1r,2r,4s,7r,8s,11r,12r,13s,16r)-7-(5-hydroxy-2-oxo-5h-furan-3-yl)-13-methoxy-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 NP0280949 ((1r,2r,4s,7r,8s,11r,12r,13s,16r)-7-(5-hydroxy-2-oxo-5h-furan-3-yl)-13-methoxy-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 NP0280949 ((1r,2r,4s,7r,8s,11r,12r,13s,16r)-7-(5-hydroxy-2-oxo-5h-furan-3-yl)-13-methoxy-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 NP0280949 ((1r,2r,4s,7r,8s,11r,12r,13s,16r)-7-(5-hydroxy-2-oxo-5h-furan-3-yl)-13-methoxy-1,8,12,13,15,15-hexamethyl-3,6,14-trioxapentacyclo[9.7.0.0²,⁴.0²,⁸.0¹²,¹⁶]octadecane-5,18-dione)