NP-MRD: Showing NP-Card for (1r,2r,4s,6r,8s,11s)-8-hydroxy-4,9-dimethyl-14-methylidene-13-oxo-5,12-dioxatricyclo[9.3.0.0⁴,⁶]tetradec-9-en-2-yl (2e)-2-methylbut-2-enoate (NP0220791)

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Record Information

Version

2.0

Created at

2022-09-05 22:12:12 UTC

Updated at

2022-09-05 22:12:12 UTC

NP-MRD ID

NP0220791

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1r,2r,4s,6r,8s,11s)-8-hydroxy-4,9-dimethyl-14-methylidene-13-oxo-5,12-dioxatricyclo[9.3.0.0⁴,⁶]tetradec-9-en-2-yl (2e)-2-methylbut-2-enoate

Description

(1R,2R,4S,6R,8S,11S)-8-hydroxy-4,9-dimethyl-14-methylidene-13-oxo-5,12-dioxatricyclo[9.3.0.0⁴,⁶]Tetradec-9-en-2-yl (2E)-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. Based on a literature review very few articles have been published on (1R,2R,4S,6R,8S,11S)-8-hydroxy-4,9-dimethyl-14-methylidene-13-oxo-5,12-dioxatricyclo[9.3.0.0⁴,⁶]Tetradec-9-en-2-yl (2E)-2-methylbut-2-enoate.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652309062200122D          

 26 28  0  0  1  0            999 V2000
    3.3327   -1.1115    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3829   -0.2880    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7462    0.2367    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9476    0.0299    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0485    1.0043    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8719    0.9541    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.4602    1.5325    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2553    1.3121    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9531    0.5445    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8436    1.8905    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.6369    2.6892    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.6386    1.6702    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8454    0.8715    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    7.0521    0.0728    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2570    0.2932    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.0367   -0.5019    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4620    0.5135    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8737   -0.0649    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.0804   -0.8636    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4921   -1.4419    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6970   -1.2216    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6988   -2.2406    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4938   -2.4609    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1105   -2.8190    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3172   -3.6177    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0786    0.1554    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  3  5  1  0  0  0  0
  6  5  1  1  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  4  0  0  0
  8 10  1  0  0  0  0
 10 11  1  1  0  0  0
 10 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  1  0  0  0
 14 15  1  0  0  0  0
 13 15  1  0  0  0  0
 15 16  1  6  0  0  0
 15 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  1  0  0  0
 19 20  1  0  0  0  0
 20 21  2  0  0  0  0
 20 22  1  0  0  0  0
 22 23  1  0  0  0  0
 22 24  2  0  0  0  0
 24 25  1  0  0  0  0
 18 26  1  0  0  0  0
 26  2  1  1  0  0  0
  6 26  1  0  0  0  0
M  END


  Mrv1652309062200122D          

 26 28  0  0  1  0            999 V2000
    3.3327   -1.1115    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3829   -0.2880    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7462    0.2367    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9476    0.0299    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0485    1.0043    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8719    0.9541    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.4602    1.5325    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2553    1.3121    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9531    0.5445    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8436    1.8905    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.6369    2.6892    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.6386    1.6702    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8454    0.8715    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    7.0521    0.0728    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2570    0.2932    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.0367   -0.5019    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4620    0.5135    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8737   -0.0649    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.0804   -0.8636    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4921   -1.4419    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6970   -1.2216    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6988   -2.2406    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4938   -2.4609    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1105   -2.8190    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3172   -3.6177    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0786    0.1554    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  3  5  1  0  0  0  0
  6  5  1  1  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  4  0  0  0
  8 10  1  0  0  0  0
 10 11  1  1  0  0  0
 10 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  1  0  0  0
 14 15  1  0  0  0  0
 13 15  1  0  0  0  0
 15 16  1  6  0  0  0
 15 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  1  0  0  0
 19 20  1  0  0  0  0
 20 21  2  0  0  0  0
 20 22  1  0  0  0  0
 22 23  1  0  0  0  0
 22 24  2  0  0  0  0
 24 25  1  0  0  0  0
 18 26  1  0  0  0  0
 26  2  1  1  0  0  0
  6 26  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0220791

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C\C=C(/C)C(=O)O[C@@H]1C[C@]2(C)O[C@@H]2C[C@H](O)C(C)=C[C@@H]2OC(=O)C(=C)[C@H]12

> <INCHI_IDENTIFIER>
InChI=1S/C20H26O6/c1-6-10(2)18(22)25-15-9-20(5)16(26-20)8-13(21)11(3)7-14-17(15)12(4)19(23)24-14/h6-7,13-17,21H,4,8-9H2,1-3,5H3/b10-6+,11-7?/t13-,14-,15+,16+,17-,20-/m0/s1

> <INCHI_KEY>
DZTWAOVNNLDWNH-BXRPTICPSA-N

> <FORMULA>
C20H26O6

> <MOLECULAR_WEIGHT>
362.422

> <EXACT_MASS>
362.172938557

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
52

> <JCHEM_AVERAGE_POLARIZABILITY>
37.72538036666788

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1R,2R,4S,6R,8S,11S)-8-hydroxy-4,9-dimethyl-14-methylidene-13-oxo-5,12-dioxatricyclo[9.3.0.0^{4,6}]tetradec-9-en-2-yl (2E)-2-methylbut-2-enoate

> <JCHEM_LOGP>
2.406761494000001

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.524404543248814

> <JCHEM_PKA_STRONGEST_BASIC>
-3.006825452782963

> <JCHEM_POLAR_SURFACE_AREA>
85.36000000000001

> <JCHEM_REFRACTIVITY>
95.53569999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1R,2R,4S,6R,8S,11S)-8-hydroxy-4,9-dimethyl-14-methylidene-13-oxo-5,12-dioxatricyclo[9.3.0.0^{4,6}]tetradec-9-en-2-yl (2E)-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       6.221  -2.075   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       6.315  -0.538   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.126   0.442   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       3.635   0.056   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0       5.690   1.875   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       7.228   1.781   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       8.326   2.861   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       9.810   2.449   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       9.246   1.016   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      10.908   3.529   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      10.522   5.020   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      12.392   3.118   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      12.778   1.627   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      13.164   0.136   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0      11.680   0.547   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      11.269  -0.937   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      10.196   0.958   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       9.098  -0.121   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       9.483  -1.612   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       8.385  -2.692   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       6.901  -2.280   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       8.771  -4.182   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      10.255  -4.594   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       7.673  -5.262   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       8.059  -6.753   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       7.613   0.290   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   26                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6                                                       
CONECT    6    5    7   26                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13                                                       
CONECT   13   12   14   15                                                  
CONECT   14   13   15                                                       
CONECT   15   14   13   16   17                                             
CONECT   16   15                                                            
CONECT   17   15   18                                                       
CONECT   18   17   19   26                                                  
CONECT   19   18   20                                                       
CONECT   20   19   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22   25                                                       
CONECT   25   24                                                            
CONECT   26   18    2    6                                                  
MASTER        0    0    0    0    0    0    0    0   26    0   56    0
END

View in JSmol

Synonyms

Value	Source
(1R,2R,4S,6R,8S,11S)-8-Hydroxy-4,9-dimethyl-14-methylidene-13-oxo-5,12-dioxatricyclo[9.3.0.0,]tetradec-9-en-2-yl (2E)-2-methylbut-2-enoic acid	Generator

Chemical Formula

C₂₀H₂₆O₆

Average Mass

362.4220 Da

Monoisotopic Mass

362.17294 Da

IUPAC Name

(1R,2R,4S,6R,8S,11S)-8-hydroxy-4,9-dimethyl-14-methylidene-13-oxo-5,12-dioxatricyclo[9.3.0.0^{4,6}]tetradec-9-en-2-yl (2E)-2-methylbut-2-enoate

Traditional Name

(1R,2R,4S,6R,8S,11S)-8-hydroxy-4,9-dimethyl-14-methylidene-13-oxo-5,12-dioxatricyclo[9.3.0.0^{4,6}]tetradec-9-en-2-yl (2E)-2-methylbut-2-enoate

CAS Registry Number

Not Available

SMILES

C\C=C(/C)C(=O)O[C@@H]1C[C@]2(C)O[C@@H]2C[C@H](O)C(C)=C[C@@H]2OC(=O)C(=C)[C@H]12

InChI Identifier

InChI=1S/C20H26O6/c1-6-10(2)18(22)25-15-9-20(5)16(26-20)8-13(21)11(3)7-14-17(15)12(4)19(23)24-14/h6-7,13-17,21H,4,8-9H2,1-3,5H3/b10-6+,11-7?/t13-,14-,15+,16+,17-,20-/m0/s1

InChI Key

DZTWAOVNNLDWNH-BXRPTICPSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Not Available

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
Fatty acid ester
Fatty acyl
Gamma butyrolactone
Dicarboxylic acid or derivatives
Alpha,beta-unsaturated carboxylic ester
Enoate ester
Tetrahydrofuran
Secondary alcohol
Lactone
Carboxylic acid ester
Oxacycle
Organoheterocyclic compound
Ether
Oxirane
Dialkyl ether
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Alcohol
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	2.41	ChemAxon
pKa (Strongest Acidic)	14.52	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	85.36 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	95.54 m³·mol⁻¹	ChemAxon
Polarizability	37.73 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	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

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

163080150

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (1r,2r,4s,6r,8s,11s)-8-hydroxy-4,9-dimethyl-14-methylidene-13-oxo-5,12-dioxatricyclo[9.3.0.0⁴,⁶]tetradec-9-en-2-yl (2e)-2-methylbut-2-enoate (NP0220791)

MOL for NP0220791 ((1r,2r,4s,6r,8s,11s)-8-hydroxy-4,9-dimethyl-14-methylidene-13-oxo-5,12-dioxatricyclo[9.3.0.0⁴,⁶]tetradec-9-en-2-yl (2e)-2-methylbut-2-enoate)

3D MOL for NP0220791 ((1r,2r,4s,6r,8s,11s)-8-hydroxy-4,9-dimethyl-14-methylidene-13-oxo-5,12-dioxatricyclo[9.3.0.0⁴,⁶]tetradec-9-en-2-yl (2e)-2-methylbut-2-enoate)

3D SDF for NP0220791 ((1r,2r,4s,6r,8s,11s)-8-hydroxy-4,9-dimethyl-14-methylidene-13-oxo-5,12-dioxatricyclo[9.3.0.0⁴,⁶]tetradec-9-en-2-yl (2e)-2-methylbut-2-enoate)

3D-SDF for NP0220791 ((1r,2r,4s,6r,8s,11s)-8-hydroxy-4,9-dimethyl-14-methylidene-13-oxo-5,12-dioxatricyclo[9.3.0.0⁴,⁶]tetradec-9-en-2-yl (2e)-2-methylbut-2-enoate)

PDB for NP0220791 ((1r,2r,4s,6r,8s,11s)-8-hydroxy-4,9-dimethyl-14-methylidene-13-oxo-5,12-dioxatricyclo[9.3.0.0⁴,⁶]tetradec-9-en-2-yl (2e)-2-methylbut-2-enoate)

3D PDB for NP0220791 ((1r,2r,4s,6r,8s,11s)-8-hydroxy-4,9-dimethyl-14-methylidene-13-oxo-5,12-dioxatricyclo[9.3.0.0⁴,⁶]tetradec-9-en-2-yl (2e)-2-methylbut-2-enoate)

SMILES for NP0220791 ((1r,2r,4s,6r,8s,11s)-8-hydroxy-4,9-dimethyl-14-methylidene-13-oxo-5,12-dioxatricyclo[9.3.0.0⁴,⁶]tetradec-9-en-2-yl (2e)-2-methylbut-2-enoate)

INCHI for NP0220791 ((1r,2r,4s,6r,8s,11s)-8-hydroxy-4,9-dimethyl-14-methylidene-13-oxo-5,12-dioxatricyclo[9.3.0.0⁴,⁶]tetradec-9-en-2-yl (2e)-2-methylbut-2-enoate)

Structure for NP0220791 ((1r,2r,4s,6r,8s,11s)-8-hydroxy-4,9-dimethyl-14-methylidene-13-oxo-5,12-dioxatricyclo[9.3.0.0⁴,⁶]tetradec-9-en-2-yl (2e)-2-methylbut-2-enoate)

3D Structure for NP0220791 ((1r,2r,4s,6r,8s,11s)-8-hydroxy-4,9-dimethyl-14-methylidene-13-oxo-5,12-dioxatricyclo[9.3.0.0⁴,⁶]tetradec-9-en-2-yl (2e)-2-methylbut-2-enoate)