NP-MRD: Showing NP-Card for Ixerin C (NP0058778)

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Record Information

Version

2.0

Created at

2022-04-28 04:07:25 UTC

Updated at

2022-04-28 04:07:25 UTC

NP-MRD ID

NP0058778

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Ixerin C

Description

[(2R,3S,4S,5R,6R)-6-{[(3aR,11aS)-6-formyl-3-methylidene-2-oxo-2H,3H,3aH,4H,5H,8H,9H,11aH-cyclodeca[b]furan-10-yl]methoxy}-3,4,5-trihydroxyoxan-2-yl]methyl 2-(4-hydroxyphenyl)acetate belongs to the class of organic compounds known as germacranolides and derivatives. These are sesquiterpene lactones with a structure based on the germacranolide skeleton, characterized by a gamma lactone fused to a 1,7-dimethylcyclodec-1-ene moiety. Ixerin C is found in Ixeris tamagawaensis. Based on a literature review very few articles have been published on [(2R,3S,4S,5R,6R)-6-{[(3aR,11aS)-6-formyl-3-methylidene-2-oxo-2H,3H,3aH,4H,5H,8H,9H,11aH-cyclodeca[b]furan-10-yl]methoxy}-3,4,5-trihydroxyoxan-2-yl]methyl 2-(4-hydroxyphenyl)acetate.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282206072D          

 40 43  0  0  1  0            999 V2000
    0.7502   -0.8834    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.4589   -0.1115    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.3652   -0.1501    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -1.3551   -1.2370    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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    0.1447   -2.2231    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9817    0.5267    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    3.1925   -1.2843    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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  1  2  1  0  0  0  0
  2  3  1  1  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
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  2  8  1  0  0  0  0
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  9 10  1  0  0  0  0
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  1 15  1  0  0  0  0
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 16 17  2  0  0  0  0
  9 18  1  0  0  0  0
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 34 37  1  0  0  0  0
 23 38  1  6  0  0  0
 22 39  1  1  0  0  0
 21 40  1  6  0  0  0
M  END

     RDKit          3D

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M  END


  Mrv1652304282206072D          

 40 43  0  0  1  0            999 V2000
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   10.1085    2.6485    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.5857    2.0103    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.7716    2.1440    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.9226    2.5149    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2239    3.4504    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5957    3.7177    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5501    2.4413    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  1  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  4  6  1  0  0  0  0
  1  6  1  6  0  0  0
  6  7  2  0  0  0  0
  2  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
  1 15  1  0  0  0  0
 13 16  1  0  0  0  0
 16 17  2  0  0  0  0
  9 18  1  0  0  0  0
 18 19  1  0  0  0  0
 20 19  1  1  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 20 25  1  0  0  0  0
 24 26  1  1  0  0  0
 26 27  1  0  0  0  0
 27 28  1  0  0  0  0
 28 29  2  0  0  0  0
 28 30  1  0  0  0  0
 30 31  1  0  0  0  0
 31 32  2  0  0  0  0
 32 33  1  0  0  0  0
 33 34  2  0  0  0  0
 34 35  1  0  0  0  0
 35 36  2  0  0  0  0
 31 36  1  0  0  0  0
 34 37  1  0  0  0  0
 23 38  1  6  0  0  0
 22 39  1  1  0  0  0
 21 40  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0058778

> <DATABASE_NAME>
NP-MRD

> <SMILES>
O[C@@H]1[C@@H](COC(=O)CC2=CC=C(O)C=C2)O[C@@H](OC\C2=C\[C@@H]3OC(=O)C(=C)[C@H]3CC\C(C=O)=C/CC2)[C@H](O)[C@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C29H34O11/c1-16-21-10-7-18(13-30)3-2-4-19(11-22(21)39-28(16)36)14-38-29-27(35)26(34)25(33)23(40-29)15-37-24(32)12-17-5-8-20(31)9-6-17/h3,5-6,8-9,11,13,21-23,25-27,29,31,33-35H,1-2,4,7,10,12,14-15H2/b18-3+,19-11+/t21-,22+,23-,25-,26+,27-,29-/m1/s1

> <INCHI_KEY>
XYJGDDXPSUNBGS-SWIYBQJHSA-N

> <FORMULA>
C29H34O11

> <MOLECULAR_WEIGHT>
558.58

> <EXACT_MASS>
558.210111915

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
74

> <JCHEM_AVERAGE_POLARIZABILITY>
57.45672297896981

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[(2R,3S,4S,5R,6R)-6-{[(3aR,11aS)-6-formyl-3-methylidene-2-oxo-2H,3H,3aH,4H,5H,8H,9H,11aH-cyclodeca[b]furan-10-yl]methoxy}-3,4,5-trihydroxyoxan-2-yl]methyl 2-(4-hydroxyphenyl)acetate

> <ALOGPS_LOGP>
1.60

> <JCHEM_LOGP>
1.7695360993333342

> <ALOGPS_LOGS>
-3.59

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.21286792158471

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.49558889445389

> <JCHEM_PKA_STRONGEST_BASIC>
-3.649085218095647

> <JCHEM_POLAR_SURFACE_AREA>
169.05

> <JCHEM_REFRACTIVITY>
140.78050000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.43e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[(2R,3S,4S,5R,6R)-6-{[(3aR,11aS)-6-formyl-3-methylidene-2-oxo-3aH,4H,5H,8H,9H,11aH-cyclodeca[b]furan-10-yl]methoxy}-3,4,5-trihydroxyoxan-2-yl]methyl (4-hydroxyphenyl)acetate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  C   UNK     0       1.400  -1.649   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.857  -0.208   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      -0.682  -0.280   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      -1.089  -1.765   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      -2.529  -2.309   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       0.198  -2.611   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.270  -4.150   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.832   0.983   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.352   0.734   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       3.896  -0.707   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       5.416  -0.957   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       5.959  -2.397   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       4.983  -3.589   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       3.464  -3.339   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       2.920  -1.898   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       5.527  -5.030   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       4.551  -6.221   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       4.328   1.925   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       5.848   1.675   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       6.824   2.867   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       6.280   4.308   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       7.256   5.499   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       8.775   5.249   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       9.319   3.809   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0       8.343   2.617   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0      10.839   3.559   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0      11.815   4.750   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0      13.334   4.501   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0      13.878   3.060   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0      14.310   5.692   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      15.830   5.443   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      16.806   6.634   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      18.325   6.385   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      18.869   4.944   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      17.893   3.753   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      16.374   4.002   0.000  0.00  0.00           C+0
HETATM   37  O   UNK     0      20.389   4.694   0.000  0.00  0.00           O+0
HETATM   38  O   UNK     0       9.751   6.441   0.000  0.00  0.00           O+0
HETATM   39  O   UNK     0       6.712   6.940   0.000  0.00  0.00           O+0
HETATM   40  O   UNK     0       4.760   4.557   0.000  0.00  0.00           O+0
CONECT    1    2    6   15                                                  
CONECT    2    1    3    8                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    1    7                                                  
CONECT    7    6                                                            
CONECT    8    2    9                                                       
CONECT    9    8   10   18                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14   16                                                  
CONECT   14   13   15                                                       
CONECT   15   14    1                                                       
CONECT   16   13   17                                                       
CONECT   17   16                                                            
CONECT   18    9   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21   25                                                  
CONECT   21   20   22   40                                                  
CONECT   22   21   23   39                                                  
CONECT   23   22   24   38                                                  
CONECT   24   23   25   26                                                  
CONECT   25   24   20                                                       
CONECT   26   24   27                                                       
CONECT   27   26   28                                                       
CONECT   28   27   29   30                                                  
CONECT   29   28                                                            
CONECT   30   28   31                                                       
CONECT   31   30   32   36                                                  
CONECT   32   31   33                                                       
CONECT   33   32   34                                                       
CONECT   34   33   35   37                                                  
CONECT   35   34   36                                                       
CONECT   36   35   31                                                       
CONECT   37   34                                                            
CONECT   38   23                                                            
CONECT   39   22                                                            
CONECT   40   21                                                            
MASTER        0    0    0    0    0    0    0    0   40    0   86    0
END

View in JSmol

Synonyms

Value	Source
[(2R,3S,4S,5R,6R)-6-{[(3ar,11as)-6-formyl-3-methylidene-2-oxo-2H,3H,3ah,4H,5H,8H,9H,11ah-cyclodeca[b]furan-10-yl]methoxy}-3,4,5-trihydroxyoxan-2-yl]methyl 2-(4-hydroxyphenyl)acetic acid	Generator

Chemical Formula

C₂₉H₃₄O₁₁

Average Mass

558.5800 Da

Monoisotopic Mass

558.21011 Da

IUPAC Name

[(2R,3S,4S,5R,6R)-6-{[(3aR,11aS)-6-formyl-3-methylidene-2-oxo-2H,3H,3aH,4H,5H,8H,9H,11aH-cyclodeca[b]furan-10-yl]methoxy}-3,4,5-trihydroxyoxan-2-yl]methyl 2-(4-hydroxyphenyl)acetate

Traditional Name

[(2R,3S,4S,5R,6R)-6-{[(3aR,11aS)-6-formyl-3-methylidene-2-oxo-3aH,4H,5H,8H,9H,11aH-cyclodeca[b]furan-10-yl]methoxy}-3,4,5-trihydroxyoxan-2-yl]methyl (4-hydroxyphenyl)acetate

CAS Registry Number

Not Available

SMILES

O[C@@H]1[C@@H](COC(=O)CC2=CC=C(O)C=C2)O[C@@H](OC\C2=C\[C@@H]3OC(=O)C(=C)[C@H]3CC\C(C=O)=C/CC2)[C@H](O)[C@H]1O

InChI Identifier

InChI=1S/C29H34O11/c1-16-21-10-7-18(13-30)3-2-4-19(11-22(21)39-28(16)36)14-38-29-27(35)26(34)25(33)23(40-29)15-37-24(32)12-17-5-8-20(31)9-6-17/h3,5-6,8-9,11,13,21-23,25-27,29,31,33-35H,1-2,4,7,10,12,14-15H2/b18-3+,19-11+/t21-,22+,23-,25-,26+,27-,29-/m1/s1

InChI Key

XYJGDDXPSUNBGS-SWIYBQJHSA-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
Ixeris tamagawaensis	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as germacranolides and derivatives. These are sesquiterpene lactones with a structure based on the germacranolide skeleton, characterized by a gamma lactone fused to a 1,7-dimethylcyclodec-1-ene moiety.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Terpene lactones

Direct Parent

Germacranolides and derivatives

Alternative Parents

Substituents

Terpene glycoside
Germacranolide
Sesquiterpenoid
Germacrane sesquiterpenoid
O-glycosyl compound
Glycosyl compound
1-hydroxy-2-unsubstituted benzenoid
Phenol
Benzenoid
Oxane
Monosaccharide
Gamma butyrolactone
Dicarboxylic acid or derivatives
Monocyclic benzene moiety
Alpha,beta-unsaturated carboxylic ester
Enoate ester
Tetrahydrofuran
Secondary alcohol
Lactone
Carboxylic acid ester
Oxacycle
Organoheterocyclic compound
Polyol
Carboxylic acid derivative
Acetal
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Aldehyde
Alcohol
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic 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	1.6	ALOGPS
logP	1.77	ChemAxon
logS	-3.6	ALOGPS
pKa (Strongest Acidic)	9.5	ChemAxon
pKa (Strongest Basic)	-3.6	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	169.05 Å²	ChemAxon
Rotatable Bond Count	9	ChemAxon
Refractivity	140.78 m³·mol⁻¹	ChemAxon
Polarizability	57.46 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	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

162996599

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Showing NP-Card for Ixerin C (NP0058778)

MOL for NP0058778 (Ixerin C)

3D MOL for NP0058778 (Ixerin C)

3D SDF for NP0058778 (Ixerin C)

3D-SDF for NP0058778 (Ixerin C)

PDB for NP0058778 (Ixerin C)

3D PDB for NP0058778 (Ixerin C)

SMILES for NP0058778 (Ixerin C)

INCHI for NP0058778 (Ixerin C)

Structure for NP0058778 (Ixerin C)

3D Structure for NP0058778 (Ixerin C)