NP-MRD: Showing NP-Card for Bakkenolide D (NP0048102)

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Record Information

Version

2.0

Created at

2022-03-17 20:51:06 UTC

Updated at

2022-03-17 20:51:06 UTC

NP-MRD ID

NP0048102

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Bakkenolide D

Description

Bakkenolide D, also known as S-fukinolide, belongs to the class of organic compounds known as terpene lactones. These are prenol lipids containing a lactone ring. Bakkenolide D is an extremely weak basic (essentially neutral) compound (based on its pKa). Outside of the human body, Bakkenolide D has been detected, but not quantified in, giant butterburs and green vegetables. This could make bakkenolide D a potential biomarker for the consumption of these foods.

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 05061308112D          

 28 30  0  0  0  0            999 V2000
    4.7432    1.0885    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5292    1.2864    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2302    4.9267    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9425    1.5055    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4576    7.2760    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4576    2.3260    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4576    3.1510    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4576    5.6260    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1721    6.0385    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4896    2.3260    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2441    2.0710    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7432    1.9135    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2742    2.0710    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3939    4.8625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7432    3.5635    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4576    4.8010    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0287    3.1510    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2441    3.4059    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2742    3.4059    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0287    2.3260    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7592    2.7385    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9032    5.5882    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.1721    4.3885    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4408    4.1021    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4896    3.1510    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9891    4.1905    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7432    4.3885    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.1721    6.8635    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
  7  6  1  0  0  0  0
  9  8  2  0  0  0  0
 12  1  1  0  0  0  0
 12  6  1  0  0  0  0
 13  2  2  0  0  0  0
 13 10  1  0  0  0  0
 14  3  1  0  0  0  0
 15  7  1  0  0  0  0
 16  8  1  0  0  0  0
 17 15  1  0  0  0  0
 18 17  1  0  0  0  0
 20  4  1  0  0  0  0
 20 11  1  0  0  0  0
 20 12  1  0  0  0  0
 20 17  1  0  0  0  0
 21 11  1  0  0  0  0
 21 13  1  0  0  0  0
 21 18  1  0  0  0  0
 21 19  1  0  0  0  0
 22 14  2  0  0  0  0
 23 16  2  0  0  0  0
 24 19  2  0  0  0  0
 25 10  1  0  0  0  0
 25 19  1  0  0  0  0
 26 14  1  0  0  0  0
 26 18  1  0  0  0  0
 27 15  1  0  0  0  0
 27 16  1  0  0  0  0
 28  5  1  0  0  0  0
 28  9  1  0  0  0  0
M  END


  Mrv0541 05061308112D          

 28 30  0  0  0  0            999 V2000
    4.7432    1.0885    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5292    1.2864    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2302    4.9267    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9425    1.5055    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4576    7.2760    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4576    2.3260    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4576    3.1510    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4576    5.6260    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1721    6.0385    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4896    2.3260    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2441    2.0710    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7432    1.9135    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2742    2.0710    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3939    4.8625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7432    3.5635    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4576    4.8010    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0287    3.1510    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2441    3.4059    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2742    3.4059    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0287    2.3260    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7592    2.7385    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9032    5.5882    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.1721    4.3885    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4408    4.1021    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4896    3.1510    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9891    4.1905    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7432    4.3885    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.1721    6.8635    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
  7  6  1  0  0  0  0
  9  8  2  0  0  0  0
 12  1  1  0  0  0  0
 12  6  1  0  0  0  0
 13  2  2  0  0  0  0
 13 10  1  0  0  0  0
 14  3  1  0  0  0  0
 15  7  1  0  0  0  0
 16  8  1  0  0  0  0
 17 15  1  0  0  0  0
 18 17  1  0  0  0  0
 20  4  1  0  0  0  0
 20 11  1  0  0  0  0
 20 12  1  0  0  0  0
 20 17  1  0  0  0  0
 21 11  1  0  0  0  0
 21 13  1  0  0  0  0
 21 18  1  0  0  0  0
 21 19  1  0  0  0  0
 22 14  2  0  0  0  0
 23 16  2  0  0  0  0
 24 19  2  0  0  0  0
 25 10  1  0  0  0  0
 25 19  1  0  0  0  0
 26 14  1  0  0  0  0
 26 18  1  0  0  0  0
 27 15  1  0  0  0  0
 27 16  1  0  0  0  0
 28  5  1  0  0  0  0
 28  9  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0048102

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CS\C=C\C(=O)OC1CCC(C)C2(C)CC3(C(OC(C)=O)C12)C(=C)COC3=O

> <INCHI_IDENTIFIER>
InChI=1S/C21H28O6S/c1-12-6-7-15(27-16(23)8-9-28-5)17-18(26-14(3)22)21(11-20(12,17)4)13(2)10-25-19(21)24/h8-9,12,15,17-18H,2,6-7,10-11H2,1,3-5H3/b9-8+

> <INCHI_KEY>
LWHLMCCRIWZBQO-CMDGGOBGSA-N

> <FORMULA>
C21H28O6S

> <MOLECULAR_WEIGHT>
408.508

> <EXACT_MASS>
408.160659318

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
42.378249333653535

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
3-(acetyloxy)-7,7a-dimethyl-4'-methylidene-2'-oxo-octahydrospiro[indene-2,3'-oxolane]-4-yl (2E)-3-(methylsulfanyl)prop-2-enoate

> <ALOGPS_LOGP>
3.15

> <JCHEM_LOGP>
2.9630240479999994

> <ALOGPS_LOGS>
-5.24

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-6.513341891013879

> <JCHEM_POLAR_SURFACE_AREA>
78.9

> <JCHEM_REFRACTIVITY>
105.28519999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.38e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-(acetyloxy)-7,7a-dimethyl-4'-methylidene-2'-oxo-hexahydro-1H-spiro[indene-2,3'-oxolane]-4-yl (2E)-3-(methylsulfanyl)prop-2-enoate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 06-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAY-13         0                                  
HETATM    1  C   UNK     0       8.854   2.032   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.721   2.401   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       7.896   9.197   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       7.359   2.810   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      10.188  13.582   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      10.188   4.342   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      10.188   5.882   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      10.188  10.502   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      11.521  11.272   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.781   4.342   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       6.056   3.866   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       8.854   3.572   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       4.245   3.866   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       6.335   9.077   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       8.854   6.652   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      10.188   8.962   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       7.520   5.882   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       6.056   6.358   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       4.245   6.358   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       7.520   4.342   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       5.151   5.112   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       5.419  10.431   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0      11.521   8.192   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0       4.556   7.657   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0       2.781   5.882   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0       5.580   7.822   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0       8.854   8.192   0.000  0.00  0.00           O+0
HETATM   28  S   UNK     0      11.521  12.812   0.000  0.00  0.00           S+0
CONECT    1   12                                                            
CONECT    2   13                                                            
CONECT    3   14                                                            
CONECT    4   20                                                            
CONECT    5   28                                                            
CONECT    6    7   12                                                       
CONECT    7    6   15                                                       
CONECT    8    9   16                                                       
CONECT    9    8   28                                                       
CONECT   10   13   25                                                       
CONECT   11   20   21                                                       
CONECT   12    1    6   20                                                  
CONECT   13    2   10   21                                                  
CONECT   14    3   22   26                                                  
CONECT   15    7   17   27                                                  
CONECT   16    8   23   27                                                  
CONECT   17   15   18   20                                                  
CONECT   18   17   21   26                                                  
CONECT   19   21   24   25                                                  
CONECT   20    4   11   12   17                                             
CONECT   21   11   13   18   19                                             
CONECT   22   14                                                            
CONECT   23   16                                                            
CONECT   24   19                                                            
CONECT   25   10   19                                                       
CONECT   26   14   18                                                       
CONECT   27   15   16                                                       
CONECT   28    5    9                                                       
MASTER        0    0    0    0    0    0    0    0   28    0   60    0
END

View in JSmol

Synonyms

Value	Source
S-Fukinolide	HMDB
3-(Acetyloxy)-7,7a-dimethyl-4'-methylidene-2'-oxo-octahydrospiro[indene-2,3'-oxolane]-4-yl (2E)-3-(methylsulfanyl)prop-2-enoic acid	Generator
3-(Acetyloxy)-7,7a-dimethyl-4'-methylidene-2'-oxo-octahydrospiro[indene-2,3'-oxolane]-4-yl (2E)-3-(methylsulphanyl)prop-2-enoate	Generator
3-(Acetyloxy)-7,7a-dimethyl-4'-methylidene-2'-oxo-octahydrospiro[indene-2,3'-oxolane]-4-yl (2E)-3-(methylsulphanyl)prop-2-enoic acid	Generator

Chemical Formula

C₂₁H₂₈O₆S

Average Mass

408.5080 Da

Monoisotopic Mass

408.16066 Da

IUPAC Name

3-(acetyloxy)-7,7a-dimethyl-4'-methylidene-2'-oxo-octahydrospiro[indene-2,3'-oxolane]-4-yl (2E)-3-(methylsulfanyl)prop-2-enoate

Traditional Name

3-(acetyloxy)-7,7a-dimethyl-4'-methylidene-2'-oxo-hexahydro-1H-spiro[indene-2,3'-oxolane]-4-yl (2E)-3-(methylsulfanyl)prop-2-enoate

CAS Registry Number

18456-03-6

SMILES

CS\C=C\C(=O)OC1CCC(C)C2(C)CC3(C(OC(C)=O)C12)C(=C)COC3=O

InChI Identifier

InChI=1S/C21H28O6S/c1-12-6-7-15(27-16(23)8-9-28-5)17-18(26-14(3)22)21(11-20(12,17)4)13(2)10-25-19(21)24/h8-9,12,15,17-18H,2,6-7,10-11H2,1,3-5H3/b9-8+

InChI Key

LWHLMCCRIWZBQO-CMDGGOBGSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Petasites japonicus	FooDB	KNAPSACK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as terpene lactones. These are prenol lipids containing a lactone ring.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Terpene lactones

Direct Parent

Terpene lactones

Alternative Parents

Substituents

Terpene lactone
Sesquiterpenoid
Tricarboxylic acid or derivatives
Gamma butyrolactone
Vinylogous thioester
Acrylic acid or derivatives
Tetrahydrofuran
Alpha,beta-unsaturated carboxylic ester
Enoate ester
Carboxylic acid ester
Lactone
Thioenolether
Oxacycle
Carboxylic acid derivative
Organoheterocyclic compound
Sulfenyl compound
Hydrocarbon derivative
Organic oxide
Organosulfur compound
Organooxygen compound
Carbonyl group
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	3.15	ALOGPS
logP	2.96	ChemAxon
logS	-5.2	ALOGPS
pKa (Strongest Basic)	-6.5	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	78.9 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	105.29 m³·mol⁻¹	ChemAxon
Polarizability	42.38 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	Yes	ChemAxon

External Links

HMDB ID

HMDB0034998

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB013602

KNApSAcK ID

C00021355

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

12299953

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Showing NP-Card for Bakkenolide D (NP0048102)

MOL for NP0048102 (Bakkenolide D)

3D MOL for NP0048102 (Bakkenolide D)

3D SDF for NP0048102 (Bakkenolide D)

3D-SDF for NP0048102 (Bakkenolide D)

PDB for NP0048102 (Bakkenolide D)

3D PDB for NP0048102 (Bakkenolide D)

SMILES for NP0048102 (Bakkenolide D)

INCHI for NP0048102 (Bakkenolide D)

Structure for NP0048102 (Bakkenolide D)

3D Structure for NP0048102 (Bakkenolide D)