NP-MRD: Showing NP-Card for (1s,2r,3r,4r,6s,8s,10s,11s)-3-hydroxy-3,8-dimethyl-2-{[(2r)-2-methylbutanoyl]oxy}-12-methylidene-9,13-dioxo-5,14-dioxatricyclo[9.3.0.0⁴,⁶]tetradecan-10-yl (2z)-2-methylbut-2-enoate (NP0229409)

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Record Information

Version

2.0

Created at

2022-09-06 09:27:10 UTC

Updated at

2022-09-06 09:27:10 UTC

NP-MRD ID

NP0229409

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1s,2r,3r,4r,6s,8s,10s,11s)-3-hydroxy-3,8-dimethyl-2-{[(2r)-2-methylbutanoyl]oxy}-12-methylidene-9,13-dioxo-5,14-dioxatricyclo[9.3.0.0⁴,⁶]tetradecan-10-yl (2z)-2-methylbut-2-enoate

Description

(1S,2R,3R,4R,6S,8S,10S,11S)-3-hydroxy-3,8-dimethyl-2-{[(2R)-2-methylbutanoyl]oxy}-12-methylidene-9,13-dioxo-5,14-dioxatricyclo[9.3.0.0⁴,⁶]Tetradecan-10-yl (2Z)-2-methylbut-2-enoate 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. (1s,2r,3r,4r,6s,8s,10s,11s)-3-hydroxy-3,8-dimethyl-2-{[(2r)-2-methylbutanoyl]oxy}-12-methylidene-9,13-dioxo-5,14-dioxatricyclo[9.3.0.0⁴,⁶]tetradecan-10-yl (2z)-2-methylbut-2-enoate is found in Duhaldea cappa. Based on a literature review very few articles have been published on (1S,2R,3R,4R,6S,8S,10S,11S)-3-hydroxy-3,8-dimethyl-2-{[(2R)-2-methylbutanoyl]oxy}-12-methylidene-9,13-dioxo-5,14-dioxatricyclo[9.3.0.0⁴,⁶]Tetradecan-10-yl (2Z)-2-methylbut-2-enoate.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309062211272D          

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M  END

     RDKit          3D

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M  END


  Mrv1652309062211272D          

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 24 25  1  6  0  0  0
 24 26  1  1  0  0  0
 24 27  1  0  0  0  0
  6 27  1  0  0  0  0
 27 28  1  1  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  6  0  0  0
 31 33  1  0  0  0  0
 33 34  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0229409

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC[C@@H](C)C(=O)O[C@@H]1[C@H]2OC(=O)C(=C)[C@@H]2[C@H](OC(=O)C(\C)=C/C)C(=O)[C@@H](C)C[C@@H]2O[C@H]2[C@@]1(C)O

> <INCHI_IDENTIFIER>
InChI=1S/C25H34O9/c1-8-11(3)22(27)32-18-16-14(6)24(29)33-19(16)21(34-23(28)12(4)9-2)25(7,30)20-15(31-20)10-13(5)17(18)26/h8,12-13,15-16,18-21,30H,6,9-10H2,1-5,7H3/b11-8-/t12-,13+,15+,16-,18+,19+,20-,21-,25-/m1/s1

> <INCHI_KEY>
YMHIUNQWQCDVJK-ZCKJMAJASA-N

> <FORMULA>
C25H34O9

> <MOLECULAR_WEIGHT>
478.538

> <EXACT_MASS>
478.220282675

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
68

> <JCHEM_AVERAGE_POLARIZABILITY>
49.23146568044157

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1S,2R,3R,4R,6S,8S,10S,11S)-3-hydroxy-3,8-dimethyl-2-{[(2R)-2-methylbutanoyl]oxy}-12-methylidene-9,13-dioxo-5,14-dioxatricyclo[9.3.0.0^{4,6}]tetradecan-10-yl (2Z)-2-methylbut-2-enoate

> <JCHEM_LOGP>
3.9164585640000005

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.040842070971564

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.880749989483622

> <JCHEM_PKA_STRONGEST_BASIC>
-3.709272864522

> <JCHEM_POLAR_SURFACE_AREA>
128.73000000000002

> <JCHEM_REFRACTIVITY>
119.27029999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1S,2R,3R,4R,6S,8S,10S,11S)-3-hydroxy-3,8-dimethyl-2-{[(2R)-2-methylbutanoyl]oxy}-12-methylidene-9,13-dioxo-5,14-dioxatricyclo[9.3.0.0^{4,6}]tetradecan-10-yl (2Z)-2-methylbut-2-enoate

> <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      -2.687  -0.771   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.090  -0.812   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.516  -2.241   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      -1.522  -3.485   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0       1.021  -2.137   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       1.396  -0.644   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.092   0.175   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.149   1.714   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -1.074   2.762   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      -1.365   4.347   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -0.380   5.593   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      -2.788   5.064   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -4.191   4.349   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -2.908   6.634   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -1.636   7.503   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       1.511   2.434   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       1.922   4.006   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       2.815   1.615   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       4.536   2.795   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       4.176   2.335   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       5.481   1.516   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       6.785   0.697   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0       5.423  -0.023   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       4.062  -0.743   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       5.371  -1.502   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       3.604  -2.519   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0       2.758   0.076   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0       3.112  -1.606   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0       4.768  -2.397   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0       4.656  -4.001   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0       6.548  -1.706   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       7.742  -0.465   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       8.144  -2.397   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       8.670  -3.925   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    7                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6                                                       
CONECT    6    5    7   27                                                  
CONECT    7    6    2    8                                                  
CONECT    8    7    9   16                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12   15                                                       
CONECT   15   14                                                            
CONECT   16    8   17   18                                                  
CONECT   17   16                                                            
CONECT   18   16   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18   21                                                       
CONECT   21   20   22   23                                                  
CONECT   22   21   23                                                       
CONECT   23   22   21   24                                                  
CONECT   24   23   25   26   27                                             
CONECT   25   24                                                            
CONECT   26   24                                                            
CONECT   27   24    6   28                                                  
CONECT   28   27   29                                                       
CONECT   29   28   30   31                                                  
CONECT   30   29                                                            
CONECT   31   29   32   33                                                  
CONECT   32   31                                                            
CONECT   33   31   34                                                       
CONECT   34   33                                                            
MASTER        0    0    0    0    0    0    0    0   34    0   72    0
END

View in JSmol

Synonyms

Value	Source
(1S,2R,3R,4R,6S,8S,10S,11S)-3-Hydroxy-3,8-dimethyl-2-{[(2R)-2-methylbutanoyl]oxy}-12-methylidene-9,13-dioxo-5,14-dioxatricyclo[9.3.0.0,]tetradecan-10-yl (2Z)-2-methylbut-2-enoic acid	Generator

Chemical Formula

C₂₅H₃₄O₉

Average Mass

478.5380 Da

Monoisotopic Mass

478.22028 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

CC[C@@H](C)C(=O)O[C@@H]1[C@H]2OC(=O)C(=C)[C@@H]2[C@H](OC(=O)C(\C)=C/C)C(=O)[C@@H](C)C[C@@H]2O[C@H]2[C@@]1(C)O

InChI Identifier

InChI=1S/C25H34O9/c1-8-11(3)22(27)32-18-16-14(6)24(29)33-19(16)21(34-23(28)12(4)9-2)25(7,30)20-15(31-20)10-13(5)17(18)26/h8,12-13,15-16,18-21,30H,6,9-10H2,1-5,7H3/b11-8-/t12-,13+,15+,16-,18+,19+,20-,21-,25-/m1/s1

InChI Key

YMHIUNQWQCDVJK-ZCKJMAJASA-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
Duhaldea cappa	LOTUS Database	35616633

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

Germacranolide
Sesquiterpenoid
Tricarboxylic acid or derivatives
Fatty acid ester
Alpha-acyloxy ketone
Fatty acyl
Gamma butyrolactone
Alpha,beta-unsaturated carboxylic ester
Enoate ester
Tertiary alcohol
Tetrahydrofuran
Carboxylic acid ester
Ketone
Lactone
Cyclic ketone
Organoheterocyclic compound
Ether
Oxirane
Dialkyl ether
Oxacycle
Carboxylic acid derivative
Carbonyl group
Organic oxygen compound
Alcohol
Organooxygen compound
Organic oxide
Hydrocarbon derivative
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

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

162947030

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (1s,2r,3r,4r,6s,8s,10s,11s)-3-hydroxy-3,8-dimethyl-2-{[(2r)-2-methylbutanoyl]oxy}-12-methylidene-9,13-dioxo-5,14-dioxatricyclo[9.3.0.0⁴,⁶]tetradecan-10-yl (2z)-2-methylbut-2-enoate (NP0229409)

MOL for NP0229409 ((1s,2r,3r,4r,6s,8s,10s,11s)-3-hydroxy-3,8-dimethyl-2-{[(2r)-2-methylbutanoyl]oxy}-12-methylidene-9,13-dioxo-5,14-dioxatricyclo[9.3.0.0⁴,⁶]tetradecan-10-yl (2z)-2-methylbut-2-enoate)

3D MOL for NP0229409 ((1s,2r,3r,4r,6s,8s,10s,11s)-3-hydroxy-3,8-dimethyl-2-{[(2r)-2-methylbutanoyl]oxy}-12-methylidene-9,13-dioxo-5,14-dioxatricyclo[9.3.0.0⁴,⁶]tetradecan-10-yl (2z)-2-methylbut-2-enoate)

3D SDF for NP0229409 ((1s,2r,3r,4r,6s,8s,10s,11s)-3-hydroxy-3,8-dimethyl-2-{[(2r)-2-methylbutanoyl]oxy}-12-methylidene-9,13-dioxo-5,14-dioxatricyclo[9.3.0.0⁴,⁶]tetradecan-10-yl (2z)-2-methylbut-2-enoate)

3D-SDF for NP0229409 ((1s,2r,3r,4r,6s,8s,10s,11s)-3-hydroxy-3,8-dimethyl-2-{[(2r)-2-methylbutanoyl]oxy}-12-methylidene-9,13-dioxo-5,14-dioxatricyclo[9.3.0.0⁴,⁶]tetradecan-10-yl (2z)-2-methylbut-2-enoate)

PDB for NP0229409 ((1s,2r,3r,4r,6s,8s,10s,11s)-3-hydroxy-3,8-dimethyl-2-{[(2r)-2-methylbutanoyl]oxy}-12-methylidene-9,13-dioxo-5,14-dioxatricyclo[9.3.0.0⁴,⁶]tetradecan-10-yl (2z)-2-methylbut-2-enoate)

3D PDB for NP0229409 ((1s,2r,3r,4r,6s,8s,10s,11s)-3-hydroxy-3,8-dimethyl-2-{[(2r)-2-methylbutanoyl]oxy}-12-methylidene-9,13-dioxo-5,14-dioxatricyclo[9.3.0.0⁴,⁶]tetradecan-10-yl (2z)-2-methylbut-2-enoate)

SMILES for NP0229409 ((1s,2r,3r,4r,6s,8s,10s,11s)-3-hydroxy-3,8-dimethyl-2-{[(2r)-2-methylbutanoyl]oxy}-12-methylidene-9,13-dioxo-5,14-dioxatricyclo[9.3.0.0⁴,⁶]tetradecan-10-yl (2z)-2-methylbut-2-enoate)

INCHI for NP0229409 ((1s,2r,3r,4r,6s,8s,10s,11s)-3-hydroxy-3,8-dimethyl-2-{[(2r)-2-methylbutanoyl]oxy}-12-methylidene-9,13-dioxo-5,14-dioxatricyclo[9.3.0.0⁴,⁶]tetradecan-10-yl (2z)-2-methylbut-2-enoate)

Structure for NP0229409 ((1s,2r,3r,4r,6s,8s,10s,11s)-3-hydroxy-3,8-dimethyl-2-{[(2r)-2-methylbutanoyl]oxy}-12-methylidene-9,13-dioxo-5,14-dioxatricyclo[9.3.0.0⁴,⁶]tetradecan-10-yl (2z)-2-methylbut-2-enoate)

3D Structure for NP0229409 ((1s,2r,3r,4r,6s,8s,10s,11s)-3-hydroxy-3,8-dimethyl-2-{[(2r)-2-methylbutanoyl]oxy}-12-methylidene-9,13-dioxo-5,14-dioxatricyclo[9.3.0.0⁴,⁶]tetradecan-10-yl (2z)-2-methylbut-2-enoate)