NP-MRD: Showing NP-Card for bakkenolide a (NP0239745)

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Record Information

Version

2.0

Created at

2022-09-06 23:24:03 UTC

Updated at

2022-09-06 23:24:03 UTC

NP-MRD ID

NP0239745

Secondary Accession Numbers

None

Natural Product Identification

Common Name

bakkenolide a

Description

Bakkenolide A belongs to the class of organic compounds known as terpene lactones. These are prenol lipids containing a lactone ring. bakkenolide a is found in Alpinia oxyphylla, Cacalia hastata, Dolichorrhiza persica, Hertia cheirifolia, Homogyne alpina, Ligularia dolichobotrys, Ligularia intermedia, Ligularia kanaitzensis, Ligularia sagitta, Ligularia subspicata, Petasites albus, Petasites frigidus and Petasites japonicus. bakkenolide a was first documented in 2012 (PMID: 22899504). Based on a literature review a small amount of articles have been published on Bakkenolide A (PMID: 34251393) (PMID: 31639086) (PMID: 27522258).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 39 41  0  0  0  0  0  0  0  0999 V2000
    3.1837    1.5190    0.2246 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9423    0.2953   -0.2033 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9199   -0.5391   -0.9467 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2095   -1.7398   -1.2662 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1286   -1.8682   -0.3917 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6056   -2.9298    0.0369 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7095   -0.5072   -0.0604 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.0833   -0.4023    1.3080 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3904   -0.6875    1.0547 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.1628   -0.0161    2.1483 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6054    0.0701    1.6746 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6121    1.1319    0.6149 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5758    0.9727   -0.4311 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.2632    1.0371   -1.7819 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7008   -0.2256   -0.3155 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.3518   -1.3458   -1.1284 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6420    0.0385   -0.9649 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3787    2.0290    0.7598 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1339    1.9758    0.0453 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7309   -0.8317   -0.2570 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2963   -0.0387   -1.8564 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2283    0.6287    1.6878 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5215   -1.1694    1.9700 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5607   -1.7804    1.1431 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0674   -0.6051    3.0672 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8027    1.0317    2.2917 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2052    0.4489    2.5286 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9705   -0.9073    1.3337 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5252    2.1196    1.1569 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6599    1.1567    0.1947 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9107    1.8831   -0.3986 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0870    0.3315   -1.8887 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7109    2.0733   -1.8354 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5314    1.0022   -2.6174 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9552   -2.2989   -0.7390 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0756   -1.2618   -2.1831 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4477   -1.3701   -0.9625 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7641    1.1391   -1.0197 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6943   -0.3592   -1.9928 H   0  0  0  0  0  0  0  0  0  0  0  0
 14 13  1  0
 13 12  1  0
 12 11  1  0
 11 10  1  0
 10  9  1  0
  9  8  1  0
  8  7  1  0
  7 17  1  0
 17 15  1  0
 15 16  1  6
  7  2  1  1
  2  1  2  3
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  2  0
 15 13  1  0
 15  9  1  0
  5  7  1  0
 14 32  1  0
 14 33  1  0
 14 34  1  0
 13 31  1  6
 12 29  1  0
 12 30  1  0
 11 27  1  0
 11 28  1  0
 10 25  1  0
 10 26  1  0
  9 24  1  6
  8 22  1  0
  8 23  1  0
 17 38  1  0
 17 39  1  0
 16 35  1  0
 16 36  1  0
 16 37  1  0
  1 18  1  0
  1 19  1  0
  3 20  1  0
  3 21  1  0
M  END


  Mrv1652309072201242D          

 17 19  0  0  1  0            999 V2000
    2.9285    1.8646    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1834    1.0799    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9680    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9680    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1834   -0.2549    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9285   -1.0396    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6985    0.4125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.2136   -0.2549    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.5152    1.6455    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2136    1.0799    0.0000 C   0  0  0  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  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  7  5  1  6  0  0  0
  2  7  1  0  0  0  0
  7  8  1  0  0  0  0
  9  8  1  1  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  6  0  0  0
 13 15  1  0  0  0  0
  9 15  1  0  0  0  0
 15 16  1  6  0  0  0
 15 17  1  0  0  0  0
  7 17  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0239745

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@H]1CCC[C@@H]2C[C@@]3(C[C@]12C)C(=C)COC3=O

> <INCHI_IDENTIFIER>
InChI=1S/C15H22O2/c1-10-5-4-6-12-7-15(9-14(10,12)3)11(2)8-17-13(15)16/h10,12H,2,4-9H2,1,3H3/t10-,12+,14+,15+/m0/s1

> <INCHI_KEY>
OVXAYHNZXBOVPV-QMGNLALYSA-N

> <FORMULA>
C15H22O2

> <MOLECULAR_WEIGHT>
234.339

> <EXACT_MASS>
234.161979948

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
39

> <JCHEM_AVERAGE_POLARIZABILITY>
26.53212844524315

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2R,3aR,4S,7aR)-3a,4-dimethyl-4'-methylidene-octahydrospiro[indene-2,3'-oxolane]-2'-one

> <JCHEM_LOGP>
3.355759895

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-7.173025305289968

> <JCHEM_POLAR_SURFACE_AREA>
26.3

> <JCHEM_REFRACTIVITY>
66.47619999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
bakkenolide A

> <JCHEM_VEBER_RULE>
1

$$$$

HEADER    PROTEIN                                 07-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   07-SEP-22         0                                  
HETATM    1  C   UNK     0       5.466   3.481   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       5.942   2.016   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       7.407   1.540   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       7.407   0.000   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       5.942  -0.476   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       5.466  -1.941   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       5.037   0.770   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.132  -0.476   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -0.000   0.000   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       2.828   3.072   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       4.132   2.016   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    7                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    2    8   17                                             
CONECT    8    7    9                                                       
CONECT    9    8   10   15                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13    9   16   17                                             
CONECT   16   15                                                            
CONECT   17   15    7                                                       
MASTER        0    0    0    0    0    0    0    0   17    0   38    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₅H₂₂O₂

Average Mass

234.3390 Da

Monoisotopic Mass

234.16198 Da

IUPAC Name

(2R,3aR,4S,7aR)-3a,4-dimethyl-4'-methylidene-octahydrospiro[indene-2,3'-oxolane]-2'-one

Traditional Name

bakkenolide A

CAS Registry Number

Not Available

SMILES

C[C@H]1CCC[C@@H]2C[C@@]3(C[C@]12C)C(=C)COC3=O

InChI Identifier

InChI=1S/C15H22O2/c1-10-5-4-6-12-7-15(9-14(10,12)3)11(2)8-17-13(15)16/h10,12H,2,4-9H2,1,3H3/t10-,12+,14+,15+/m0/s1

InChI Key

OVXAYHNZXBOVPV-QMGNLALYSA-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
Alpinia oxyphylla	LOTUS Database	35616633
Cacalia hastata	LOTUS Database	35616633
Dolichorrhiza persica	LOTUS Database	35616633
Hertia cheirifolia	LOTUS Database	35616633
Homogyne alpina	LOTUS Database	35616633
Ligularia dolichobotrys	LOTUS Database	35616633
Ligularia intermedia	LOTUS Database	35616633
Ligularia kanaitzensis	LOTUS Database	35616633
Ligularia sagitta	LOTUS Database	35616633
Ligularia subspicata	LOTUS Database	35616633
Petasites albus	LOTUS Database	35616633
Petasites frigidus	LOTUS Database	35616633
Petasites japonicus	LOTUS Database	35616633

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
Gamma butyrolactone
Tetrahydrofuran
Lactone
Carboxylic acid ester
Oxacycle
Organoheterocyclic compound
Monocarboxylic acid or derivatives
Carboxylic acid derivative
Organic oxide
Organic oxygen compound
Organooxygen compound
Carbonyl group
Hydrocarbon derivative
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

sesquiterpenoid (CHEBI:2984 )
Sesquiterpenoids (C15) (C09350 )

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	3.36	ChemAxon
pKa (Strongest Basic)	-7.2	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	1	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	26.3 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	66.48 m³·mol⁻¹	ChemAxon
Polarizability	26.53 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	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

C00003225

Chemspider ID

390687

KEGG Compound ID

C09350

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

442173

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

rw1384261

References

General References

Uesugi S, Hakozaki M, Kanno Y, Takahashi H, Kudo Y, Kimura KI, Yamada H, Yano A: A yeast-based screening system identified bakkenolide B contained in Petasites japonicus as an inhibitor of interleukin-2 production in a human T cell line. Biosci Biotechnol Biochem. 2021 Sep 22;85(10):2153-2160. doi: 10.1093/bbb/zbab130. [PubMed:34251393 ]
Jerkovic I, Males Z, Friscic M: Actualities in the phytochemical research on selected terpenes. Acta Pharm. 2019 Dec 1;69(4):533-540. doi: 10.2478/acph-2019-0036. [PubMed:31639086 ]
Zhang L, Hong Z, Zhang RR, Sun XZ, Yuan YF, Hu J, Wang X: Bakkenolide A inhibits leukemia by regulation of HDAC3 and PI3K/Akt-related signaling pathways. Biomed Pharmacother. 2016 Oct;83:958-966. doi: 10.1016/j.biopha.2016.07.049. Epub 2016 Aug 12. [PubMed:27522258 ]
Pei L, Dai D, Bao Y, Chen F, Zheng J, Li J, Liu S, Chen X: Determination of bakkenolide A in rat plasma using liquid chromatography/tandem mass spectrometry and its application to a pharmacokinetic study. J Mass Spectrom. 2012 Aug;47(8):962-8. doi: 10.1002/jms.3042. [PubMed:22899504 ]
LOTUS database [Link]

Showing NP-Card for bakkenolide a (NP0239745)

MOL for NP0239745 (bakkenolide a)

3D MOL for NP0239745 (bakkenolide a)

3D SDF for NP0239745 (bakkenolide a)

3D-SDF for NP0239745 (bakkenolide a)

PDB for NP0239745 (bakkenolide a)

3D PDB for NP0239745 (bakkenolide a)

SMILES for NP0239745 (bakkenolide a)

INCHI for NP0239745 (bakkenolide a)

Structure for NP0239745 (bakkenolide a)

3D Structure for NP0239745 (bakkenolide a)