NP-MRD: Showing NP-Card for 2beta,9xi-Dihydroxy-8-oxo-1(10),4,11(13)-germacratrien-12,6alpha-olide (NP0335370)

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Record Information

Version

2.0

Created at

2024-09-11 01:17:35 UTC

Updated at

2024-09-11 01:17:35 UTC

NP-MRD ID

NP0335370

Secondary Accession Numbers

None

Natural Product Identification

Common Name

2beta,9xi-Dihydroxy-8-oxo-1(10),4,11(13)-germacratrien-12,6alpha-olide

Description

2Beta,9xi-Dihydroxy-8-oxo-1(10),4,11(13)-germacratrien-12,6alpha-olide 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 2beta,9xi-Dihydroxy-8-oxo-1(10),4,11(13)-germacratrien-12,6alpha-olide.

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 05262303492D          

 20 21  0  0  0  0            999 V2000
    5.0298    3.2521    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6722   -0.4735    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8558   -0.0022    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7983    1.8420    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6929    2.7476    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9037    0.9365    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5070    2.6139    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3809    0.2983    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8173    0.8219    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6124    1.7084    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1701    2.1093    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4614    1.3375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5668    0.4320    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2755    1.2038    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1279    1.2751    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1352    2.3466    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0440   -0.2062    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0735    1.4129    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3561    0.9838    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3460    2.0708    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  7  1  1  0  0  0  0
  7  4  1  0  0  0  0
  7  5  2  0  0  0  0
  8  2  1  0  0  0  0
  8  6  2  0  0  0  0
  9  3  2  0  0  0  0
 10  4  1  0  0  0  0
 10  6  1  0  0  0  0
 11  5  1  0  0  0  0
 12  9  1  0  0  0  0
 12 11  1  0  0  0  0
 13  8  1  0  0  0  0
 14 12  1  0  0  0  0
 14 13  1  0  0  0  0
 15  9  1  0  0  0  0
 16 10  1  0  0  0  0
 17 13  2  0  0  0  0
 18 14  1  0  0  0  0
 19 15  2  0  0  0  0
 20 11  1  0  0  0  0
 20 15  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0335370

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C\C1=C\C2OC(=O)C(=C)C2C(O)C(=O)\C(C)=C/C(O)C1

> <INCHI_IDENTIFIER>
InChI=1/C15H18O5/c1-7-4-10(16)6-8(2)13(17)14(18)12-9(3)15(19)20-11(12)5-7/h5-6,10-12,14,16,18H,3-4H2,1-2H3/b7-5-,8-6-

> <INCHI_KEY>
BPDUDXQLWXZOHB-SFECMWDFNA-N

> <FORMULA>
C15H18O5

> <MOLECULAR_WEIGHT>
278.304

> <EXACT_MASS>
278.11542368

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
38

> <JCHEM_AVERAGE_POLARIZABILITY>
28.218371708567872

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
4,8-dihydroxy-6,10-dimethyl-3-methylidene-2H,3H,3aH,4H,5H,8H,9H,11aH-cyclodeca[b]furan-2,5-dione

> <JCHEM_LOGP>
1.0885630246666667

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.786303338214429

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.968509240910295

> <JCHEM_PKA_STRONGEST_BASIC>
-2.8966896247174283

> <JCHEM_POLAR_SURFACE_AREA>
83.83

> <JCHEM_REFRACTIVITY>
73.54849999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
4,8-dihydroxy-6,10-dimethyl-3-methylidene-3aH,4H,8H,9H,11aH-cyclodeca[b]furan-2,5-dione

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 26-MAY-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   26-MAY-23         0                                  
HETATM    1  C   UNK     0       9.389   6.071   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      10.588  -0.884   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.331  -0.004   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       8.957   3.438   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       6.893   5.129   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      11.020   1.748   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       8.413   4.879   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      10.044   0.557   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       5.259   1.534   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      10.476   3.189   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       5.918   3.937   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       6.461   2.497   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       8.525   0.806   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       7.981   2.247   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       3.972   2.380   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      11.452   4.380   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       7.549  -0.385   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       9.471   2.637   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       2.531   1.836   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       4.379   3.865   0.000  0.00  0.00           O+0
CONECT    1    7                                                            
CONECT    2    8                                                            
CONECT    3    9                                                            
CONECT    4    7   10                                                       
CONECT    5    7   11                                                       
CONECT    6    8   10                                                       
CONECT    7    1    4    5                                                  
CONECT    8    2    6   13                                                  
CONECT    9    3   12   15                                                  
CONECT   10    4    6   16                                                  
CONECT   11    5   12   20                                                  
CONECT   12    9   11   14                                                  
CONECT   13    8   14   17                                                  
CONECT   14   12   13   18                                                  
CONECT   15    9   19   20                                                  
CONECT   16   10                                                            
CONECT   17   13                                                            
CONECT   18   14                                                            
CONECT   19   15                                                            
CONECT   20   11   15                                                       
MASTER        0    0    0    0    0    0    0    0   20    0   42    0
END

View in JSmol

Synonyms

Value	Source
2b,9XI-dihydroxy-8-oxo-1(10),4,11(13)-germacratrien-12,6a-olide	Generator
2Β,9xi-dihydroxy-8-oxo-1(10),4,11(13)-germacratrien-12,6α-olide	Generator

Chemical Formula

C₁₅H₁₈O₅

Average Mass

278.3040 Da

Monoisotopic Mass

278.11542 Da

IUPAC Name

4,8-dihydroxy-6,10-dimethyl-3-methylidene-2H,3H,3aH,4H,5H,8H,9H,11aH-cyclodeca[b]furan-2,5-dione

Traditional Name

4,8-dihydroxy-6,10-dimethyl-3-methylidene-3aH,4H,8H,9H,11aH-cyclodeca[b]furan-2,5-dione

CAS Registry Number

Not Available

SMILES

C\C1=C\C2OC(=O)C(=C)C2C(O)C(=O)\C(C)=C/C(O)C1

InChI Identifier

InChI=1/C15H18O5/c1-7-4-10(16)6-8(2)13(17)14(18)12-9(3)15(19)20-11(12)5-7/h5-6,10-12,14,16,18H,3-4H2,1-2H3/b7-5-,8-6-

InChI Key

BPDUDXQLWXZOHB-SFECMWDFNA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Not Available

Chemical Taxonomy

Description

This compound 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
Tetrahydrofuran
Enoate ester
Alpha,beta-unsaturated carboxylic ester
Cyclic ketone
Secondary alcohol
Lactone
Ketone
Carboxylic acid ester
Oxacycle
Monocarboxylic acid or derivatives
Carboxylic acid derivative
Organoheterocyclic compound
Alcohol
Organooxygen compound
Hydrocarbon derivative
Organic oxide
Organic oxygen compound
Carbonyl group
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	1.09	ChemAxon
pKa (Strongest Acidic)	12.97	ChemAxon
pKa (Strongest Basic)	-2.9	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	83.83 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	73.55 m³·mol⁻¹	ChemAxon
Polarizability	28.22 Å³	ChemAxon
Number of Rings	2	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

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for 2beta,9xi-Dihydroxy-8-oxo-1(10),4,11(13)-germacratrien-12,6alpha-olide (NP0335370)

MOL for NP0335370 (2beta,9xi-Dihydroxy-8-oxo-1(10),4,11(13)-germacratrien-12,6alpha-olide)

3D MOL for NP0335370 (2beta,9xi-Dihydroxy-8-oxo-1(10),4,11(13)-germacratrien-12,6alpha-olide)

3D SDF for NP0335370 (2beta,9xi-Dihydroxy-8-oxo-1(10),4,11(13)-germacratrien-12,6alpha-olide)

3D-SDF for NP0335370 (2beta,9xi-Dihydroxy-8-oxo-1(10),4,11(13)-germacratrien-12,6alpha-olide)

PDB for NP0335370 (2beta,9xi-Dihydroxy-8-oxo-1(10),4,11(13)-germacratrien-12,6alpha-olide)

3D PDB for NP0335370 (2beta,9xi-Dihydroxy-8-oxo-1(10),4,11(13)-germacratrien-12,6alpha-olide)

SMILES for NP0335370 (2beta,9xi-Dihydroxy-8-oxo-1(10),4,11(13)-germacratrien-12,6alpha-olide)

INCHI for NP0335370 (2beta,9xi-Dihydroxy-8-oxo-1(10),4,11(13)-germacratrien-12,6alpha-olide)

Structure for NP0335370 (2beta,9xi-Dihydroxy-8-oxo-1(10),4,11(13)-germacratrien-12,6alpha-olide)

3D Structure for NP0335370 (2beta,9xi-Dihydroxy-8-oxo-1(10),4,11(13)-germacratrien-12,6alpha-olide)