NP-MRD: Showing NP-Card for (1s,2s,4r,7e,11s)-4,8-dimethyl-12-methylidene-3,14-dioxatricyclo[9.3.0.0²,⁴]tetradec-7-ene-9,13-dione (NP0197093)

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Record Information

Version

2.0

Created at

2022-09-04 15:17:38 UTC

Updated at

2022-09-04 15:17:38 UTC

NP-MRD ID

NP0197093

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1s,2s,4r,7e,11s)-4,8-dimethyl-12-methylidene-3,14-dioxatricyclo[9.3.0.0²,⁴]tetradec-7-ene-9,13-dione

Description

NSC672120, also known as parthenolid-9-one, 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,2s,4r,7e,11s)-4,8-dimethyl-12-methylidene-3,14-dioxatricyclo[9.3.0.0²,⁴]tetradec-7-ene-9,13-dione is found in Anvillea garcinii. Based on a literature review very few articles have been published on NSC672120.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652309042217172D          

 19 21  0  0  1  0            999 V2000
    5.0951   -1.6841    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3518   -1.3260    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2047   -0.5142    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7749    0.0820    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3871   -0.4034    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0291   -1.1466    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.6253   -1.7168    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.7725   -2.5286    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4144   -3.2718    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8052   -3.9984    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5969   -3.1610    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4497   -2.3492    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8703   -3.5518    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2741   -2.9816    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1269   -2.1698    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4850   -1.4266    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.6835   -1.2308    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5098   -0.6019    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2115   -1.0357    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  2  1  6  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
 11 12  1  0  0  0  0
 11 13  2  0  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  6  0  0  0
 16 18  1  0  0  0  0
 19 18  1  1  0  0  0
  6 19  1  0  0  0  0
 16 19  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0197093

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C\C1=C/CC[C@@]2(C)O[C@H]2[C@H]2OC(=O)C(=C)[C@@H]2CC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C15H18O4/c1-8-5-4-6-15(3)13(19-15)12-10(7-11(8)16)9(2)14(17)18-12/h5,10,12-13H,2,4,6-7H2,1,3H3/b8-5+/t10-,12-,13-,15+/m0/s1

> <INCHI_KEY>
MZDVWXBIIWIBTB-BPWSPTIZSA-N

> <FORMULA>
C15H18O4

> <MOLECULAR_WEIGHT>
262.305

> <EXACT_MASS>
262.12050906

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
37

> <JCHEM_AVERAGE_POLARIZABILITY>
27.01575950445755

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1S,2S,4R,7E,11S)-4,8-dimethyl-12-methylidene-3,14-dioxatricyclo[9.3.0.0^{2,4}]tetradec-7-ene-9,13-dione

> <JCHEM_LOGP>
2.4040092370000004

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
17.459561843958895

> <JCHEM_PKA_STRONGEST_BASIC>
-4.091642177684822

> <JCHEM_POLAR_SURFACE_AREA>
55.900000000000006

> <JCHEM_REFRACTIVITY>
69.24609999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1S,2S,4R,7E,11S)-4,8-dimethyl-12-methylidene-3,14-dioxatricyclo[9.3.0.0^{2,4}]tetradec-7-ene-9,13-dione

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 04-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-22         0                                  
HETATM    1  C   UNK     0       9.511  -3.144   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       8.123  -2.475   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       7.849  -0.960   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       8.913   0.153   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0       6.323  -0.753   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       5.654  -2.140   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       6.767  -3.205   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       7.042  -4.720   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       6.374  -6.107   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       7.103  -7.464   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       4.847  -5.900   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.573  -4.385   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       3.491  -6.630   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       2.378  -5.566   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       2.104  -4.050   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       2.772  -2.663   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       1.276  -2.298   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       2.818  -1.124   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       4.128  -1.933   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   19                                                  
CONECT    7    6    2    8                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17   18   19                                             
CONECT   17   16                                                            
CONECT   18   16   19                                                       
CONECT   19   18    6   16                                                  
MASTER        0    0    0    0    0    0    0    0   19    0   42    0
END

View in JSmol

Synonyms

Value	Source
cis-Parthenolid-9-one	MeSH
Parthenolid-9-one	MeSH

Chemical Formula

C₁₅H₁₈O₄

Average Mass

262.3050 Da

Monoisotopic Mass

262.12051 Da

IUPAC Name

(1S,2S,4R,7E,11S)-4,8-dimethyl-12-methylidene-3,14-dioxatricyclo[9.3.0.0^{2,4}]tetradec-7-ene-9,13-dione

Traditional Name

(1S,2S,4R,7E,11S)-4,8-dimethyl-12-methylidene-3,14-dioxatricyclo[9.3.0.0^{2,4}]tetradec-7-ene-9,13-dione

CAS Registry Number

Not Available

SMILES

C\C1=C/CC[C@@]2(C)O[C@H]2[C@H]2OC(=O)C(=C)[C@@H]2CC1=O

InChI Identifier

InChI=1S/C15H18O4/c1-8-5-4-6-15(3)13(19-15)12-10(7-11(8)16)9(2)14(17)18-12/h5,10,12-13H,2,4,6-7H2,1,3H3/b8-5+/t10-,12-,13-,15+/m0/s1

InChI Key

MZDVWXBIIWIBTB-BPWSPTIZSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Anvillea garcinii	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
Germacrane sesquiterpenoid
Sesquiterpenoid
Gamma butyrolactone
Alpha,beta-unsaturated carboxylic ester
Enoate ester
Oxolane
Carboxylic acid ester
Ketone
Cyclic ketone
Lactone
Carboxylic acid derivative
Dialkyl ether
Oxirane
Ether
Oxacycle
Organoheterocyclic compound
Monocarboxylic acid or derivatives
Organic oxide
Hydrocarbon derivative
Carbonyl group
Organooxygen compound
Organic oxygen compound
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	2.4	ChemAxon
pKa (Strongest Acidic)	17.46	ChemAxon
pKa (Strongest Basic)	-4.1	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	55.9 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	69.25 m³·mol⁻¹	ChemAxon
Polarizability	27.02 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

16737370

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

10445414

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (1s,2s,4r,7e,11s)-4,8-dimethyl-12-methylidene-3,14-dioxatricyclo[9.3.0.0²,⁴]tetradec-7-ene-9,13-dione (NP0197093)

MOL for NP0197093 ((1s,2s,4r,7e,11s)-4,8-dimethyl-12-methylidene-3,14-dioxatricyclo[9.3.0.0²,⁴]tetradec-7-ene-9,13-dione)

3D MOL for NP0197093 ((1s,2s,4r,7e,11s)-4,8-dimethyl-12-methylidene-3,14-dioxatricyclo[9.3.0.0²,⁴]tetradec-7-ene-9,13-dione)

3D SDF for NP0197093 ((1s,2s,4r,7e,11s)-4,8-dimethyl-12-methylidene-3,14-dioxatricyclo[9.3.0.0²,⁴]tetradec-7-ene-9,13-dione)

3D-SDF for NP0197093 ((1s,2s,4r,7e,11s)-4,8-dimethyl-12-methylidene-3,14-dioxatricyclo[9.3.0.0²,⁴]tetradec-7-ene-9,13-dione)

PDB for NP0197093 ((1s,2s,4r,7e,11s)-4,8-dimethyl-12-methylidene-3,14-dioxatricyclo[9.3.0.0²,⁴]tetradec-7-ene-9,13-dione)

3D PDB for NP0197093 ((1s,2s,4r,7e,11s)-4,8-dimethyl-12-methylidene-3,14-dioxatricyclo[9.3.0.0²,⁴]tetradec-7-ene-9,13-dione)

SMILES for NP0197093 ((1s,2s,4r,7e,11s)-4,8-dimethyl-12-methylidene-3,14-dioxatricyclo[9.3.0.0²,⁴]tetradec-7-ene-9,13-dione)

INCHI for NP0197093 ((1s,2s,4r,7e,11s)-4,8-dimethyl-12-methylidene-3,14-dioxatricyclo[9.3.0.0²,⁴]tetradec-7-ene-9,13-dione)

Structure for NP0197093 ((1s,2s,4r,7e,11s)-4,8-dimethyl-12-methylidene-3,14-dioxatricyclo[9.3.0.0²,⁴]tetradec-7-ene-9,13-dione)

3D Structure for NP0197093 ((1s,2s,4r,7e,11s)-4,8-dimethyl-12-methylidene-3,14-dioxatricyclo[9.3.0.0²,⁴]tetradec-7-ene-9,13-dione)