NP-MRD: Showing NP-Card for Ixerin I (NP0073562)

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Record Information

Version

2.0

Created at

2022-04-28 18:47:26 UTC

Updated at

2022-04-28 18:47:26 UTC

NP-MRD ID

NP0073562

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Ixerin I

Description

[(3AR,11aR)-3-methylidene-2-oxo-10-({[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)-2H,3H,3aH,4H,5H,8H,9H,11aH-cyclodeca[b]furan-6-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 I is found in Ixeris tamagawaensis Kitam. Based on a literature review very few articles have been published on [(3aR,11aR)-3-methylidene-2-oxo-10-({[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)-2H,3H,3aH,4H,5H,8H,9H,11aH-cyclodeca[b]furan-6-yl]methyl 2-(4-hydroxyphenyl)acetate.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282220472D          

 40 43  0  0  1  0            999 V2000
    5.6124    1.7084    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


  Mrv1652304282220472D          

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    6.2548   -2.0172    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.5917   -1.5127    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8830   -2.2845    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.6971   -2.4182    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.9884   -3.1901    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.4656   -3.8283    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6515   -3.6946    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.3602   -2.9228    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.7569   -4.6001    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
  1 10  1  0  0  0  0
  9 11  1  0  0  0  0
 11 12  1  0  0  0  0
 13 12  1  1  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 13 18  1  0  0  0  0
 18 19  1  1  0  0  0
 17 20  1  6  0  0  0
 16 21  1  1  0  0  0
 15 22  1  6  0  0  0
 22 23  1  0  0  0  0
  7 24  1  6  0  0  0
 24 25  1  0  0  0  0
 25 26  2  0  0  0  0
 25 27  1  0  0  0  0
  6 27  1  6  0  0  0
 27 28  2  0  0  0  0
  3 29  1  0  0  0  0
 29 30  1  0  0  0  0
 30 31  1  0  0  0  0
 31 32  2  0  0  0  0
 31 33  1  0  0  0  0
 33 34  1  0  0  0  0
 34 35  2  0  0  0  0
 35 36  1  0  0  0  0
 36 37  2  0  0  0  0
 37 38  1  0  0  0  0
 38 39  2  0  0  0  0
 34 39  1  0  0  0  0
 37 40  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0073562

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC[C@H]1O[C@H](OC\C2=C\[C@H]3OC(=O)C(=C)[C@H]3CC\C(COC(=O)CC3=CC=C(O)C=C3)=C/CC2)[C@H](O)[C@@H](O)[C@@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C29H36O11/c1-16-21-10-7-18(14-37-24(32)12-17-5-8-20(31)9-6-17)3-2-4-19(11-22(21)39-28(16)36)15-38-29-27(35)26(34)25(33)23(13-30)40-29/h3,5-6,8-9,11,21-23,25-27,29-31,33-35H,1-2,4,7,10,12-15H2/b18-3+,19-11+/t21-,22-,23-,25-,26+,27-,29+/m1/s1

> <INCHI_KEY>
PWQMKQMDXFLIOW-BIBNWVPVSA-N

> <FORMULA>
C29H36O11

> <MOLECULAR_WEIGHT>
560.596

> <EXACT_MASS>
560.225761979

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
76

> <JCHEM_AVERAGE_POLARIZABILITY>
57.32226986037659

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
1.16

> <JCHEM_LOGP>
1.4556885960000003

> <ALOGPS_LOGS>
-3.53

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.211262978348877

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.495585680832438

> <JCHEM_PKA_STRONGEST_BASIC>
-2.981083552309202

> <JCHEM_POLAR_SURFACE_AREA>
172.20999999999998

> <JCHEM_REFRACTIVITY>
141.76339999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.66e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[(3aR,11aR)-3-methylidene-2-oxo-10-({[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)-3aH,4H,5H,8H,9H,11aH-cyclodeca[b]furan-6-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      10.476   3.189   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      11.020   1.748   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      10.044   0.557   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       8.525   0.806   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       7.981   2.247   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.461   2.497   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       5.917   3.937   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       6.893   5.129   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       8.413   4.879   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       8.957   3.438   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       9.389   6.071   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       8.845   7.511   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       9.821   8.703   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       9.277  10.144   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0      10.253  11.335   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      11.773  11.085   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      12.317   9.645   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      11.341   8.453   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      11.884   7.012   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0      13.836   9.395   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0      12.749  12.277   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       9.709  12.776   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0      10.685  13.967   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0       4.379   3.866   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0       3.972   2.380   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       2.531   1.836   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0       5.259   1.534   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       5.331  -0.004   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      10.588  -0.884   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0      12.108  -1.133   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0      12.652  -2.574   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0      11.676  -3.766   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0      14.171  -2.824   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      14.715  -4.264   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      16.235  -4.514   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      16.778  -5.955   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0      15.802  -7.146   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0      14.283  -6.897   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0      13.739  -5.456   0.000  0.00  0.00           C+0
HETATM   40  O   UNK     0      16.346  -8.587   0.000  0.00  0.00           O+0
CONECT    1    2   10                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4   29                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7   27                                                  
CONECT    7    6    8   24                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10   11                                                  
CONECT   10    9    1                                                       
CONECT   11    9   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14   18                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16   22                                                  
CONECT   16   15   17   21                                                  
CONECT   17   16   18   20                                                  
CONECT   18   17   13   19                                                  
CONECT   19   18                                                            
CONECT   20   17                                                            
CONECT   21   16                                                            
CONECT   22   15   23                                                       
CONECT   23   22                                                            
CONECT   24    7   25                                                       
CONECT   25   24   26   27                                                  
CONECT   26   25                                                            
CONECT   27   25    6   28                                                  
CONECT   28   27                                                            
CONECT   29    3   30                                                       
CONECT   30   29   31                                                       
CONECT   31   30   32   33                                                  
CONECT   32   31                                                            
CONECT   33   31   34                                                       
CONECT   34   33   35   39                                                  
CONECT   35   34   36                                                       
CONECT   36   35   37                                                       
CONECT   37   36   38   40                                                  
CONECT   38   37   39                                                       
CONECT   39   38   34                                                       
CONECT   40   37                                                            
MASTER        0    0    0    0    0    0    0    0   40    0   86    0
END

View in JSmol

Synonyms

Value	Source
[(3AR,11ar)-3-methylidene-2-oxo-10-({[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)-2H,3H,3ah,4H,5H,8H,9H,11ah-cyclodeca[b]furan-6-yl]methyl 2-(4-hydroxyphenyl)acetic acid	Generator

Chemical Formula

C₂₉H₃₆O₁₁

Average Mass

560.5960 Da

Monoisotopic Mass

560.22576 Da

IUPAC Name

[(3aR,11aR)-3-methylidene-2-oxo-10-({[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)-2H,3H,3aH,4H,5H,8H,9H,11aH-cyclodeca[b]furan-6-yl]methyl 2-(4-hydroxyphenyl)acetate

Traditional Name

[(3aR,11aR)-3-methylidene-2-oxo-10-({[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)-3aH,4H,5H,8H,9H,11aH-cyclodeca[b]furan-6-yl]methyl (4-hydroxyphenyl)acetate

CAS Registry Number

Not Available

SMILES

OC[C@H]1O[C@H](OC\C2=C\[C@H]3OC(=O)C(=C)[C@H]3CC\C(COC(=O)CC3=CC=C(O)C=C3)=C/CC2)[C@H](O)[C@@H](O)[C@@H]1O

InChI Identifier

InChI=1S/C29H36O11/c1-16-21-10-7-18(14-37-24(32)12-17-5-8-20(31)9-6-17)3-2-4-19(11-22(21)39-28(16)36)15-38-29-27(35)26(34)25(33)23(13-30)40-29/h3,5-6,8-9,11,21-23,25-27,29-31,33-35H,1-2,4,7,10,12-15H2/b18-3+,19-11+/t21-,22-,23-,25-,26+,27-,29+/m1/s1

InChI Key

PWQMKQMDXFLIOW-BIBNWVPVSA-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 Kitam.	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
Hexose monosaccharide
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
Primary alcohol
Organooxygen compound
Carbonyl group
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	1.16	ALOGPS
logP	1.46	ChemAxon
logS	-3.5	ALOGPS
pKa (Strongest Acidic)	9.5	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	172.21 Å²	ChemAxon
Rotatable Bond Count	9	ChemAxon
Refractivity	141.76 m³·mol⁻¹	ChemAxon
Polarizability	57.32 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

163027576

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Ixerin I (NP0073562)

MOL for NP0073562 (Ixerin I)

3D MOL for NP0073562 (Ixerin I)

3D SDF for NP0073562 (Ixerin I)

3D-SDF for NP0073562 (Ixerin I)

PDB for NP0073562 (Ixerin I)

3D PDB for NP0073562 (Ixerin I)

SMILES for NP0073562 (Ixerin I)

INCHI for NP0073562 (Ixerin I)

Structure for NP0073562 (Ixerin I)

3D Structure for NP0073562 (Ixerin I)