NP-MRD: Showing NP-Card for cardivin d (NP0291038)

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Record Information

Version

2.0

Created at

2022-09-09 21:58:48 UTC

Updated at

2022-09-09 21:58:48 UTC

NP-MRD ID

NP0291038

Secondary Accession Numbers

None

Natural Product Identification

Common Name

cardivin d

Description

Cardivin D 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. cardivin d is found in Carpesium divaricatum. It was first documented in 2022 (PMID: 36115642). Based on a literature review a significant number of articles have been published on cardivin D (PMID: 36115617) (PMID: 36115535) (PMID: 36115406) (PMID: 36115405).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309092223582D          

 32 33  0  0  1  0            999 V2000
    1.8304   -1.8899    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3460   -1.2458    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1279   -0.4501    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3561   -0.1588    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8173    0.0031    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4614   -0.5125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.2755   -0.3788    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.7527    0.2594    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0440    1.0312    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2064    1.1303    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5212    1.6694    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8125    2.4413    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7071    1.5358    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5668    0.3930    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.4616    1.2113    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8310    1.1746    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3809    0.5267    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9037   -0.1115    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.7178    0.0221    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.6124   -0.8834    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7983   -1.0170    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.0002   -0.8080    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5070   -1.7889    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0298   -2.4271    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6929   -1.9226    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.4015   -2.6944    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9243   -3.3326    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    3.1701   -1.2843    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
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  7 14  1  0  0  0  0
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 32  2  1  6  0  0  0
  6 32  1  0  0  0  0
M  END

     RDKit          3D

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   -0.2691    3.6137    0.6862 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.3750    4.9543    1.1946 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9213    3.0771    1.3541 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5618    1.8400    0.7968 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.0277    1.7539    1.2899 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6605    1.7805   -0.6639 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8362    2.7762   -1.3104 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5455    0.4869   -1.3640 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.6984   -0.2920   -1.0080 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5492   -0.8193   -1.9475 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2861   -0.5971   -3.1583 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7561   -1.6351   -1.5637 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END


  Mrv1652309092223582D          

 32 33  0  0  1  0            999 V2000
    1.8304   -1.8899    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3460   -1.2458    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1279   -0.4501    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3561   -0.1588    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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    3.4614   -0.5125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.2755   -0.3788    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
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    4.7983   -1.0170    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.0002   -0.8080    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5070   -1.7889    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0298   -2.4271    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6929   -1.9226    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
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    4.7384   -3.1990    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6330   -4.1045    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1558   -4.7427    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8189   -4.2381    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1701   -1.2843    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
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M  END
> <DATABASE_ID>
NP0291038

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)C(=O)O[C@H]1[C@H]2[C@@H](OC(=O)C2=C)[C@H](OC(=O)C(C)C)[C@@](C)(O)C[C@@H](O)C[C@H](C)C1=O

> <INCHI_IDENTIFIER>
InChI=1S/C23H34O9/c1-10(2)20(26)30-17-15-13(6)22(28)31-18(15)19(32-21(27)11(3)4)23(7,29)9-14(24)8-12(5)16(17)25/h10-12,14-15,17-19,24,29H,6,8-9H2,1-5,7H3/t12-,14-,15-,17-,18+,19-,23-/m0/s1

> <INCHI_KEY>
WOJZAWJFEPVGSB-CHYAZBGWSA-N

> <FORMULA>
C23H34O9

> <MOLECULAR_WEIGHT>
454.516

> <EXACT_MASS>
454.220282675

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
66

> <JCHEM_AVERAGE_POLARIZABILITY>
46.59835693481998

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(3aR,4S,6S,8S,10S,11S,11aR)-8,10-dihydroxy-6,10-dimethyl-3-methylidene-4-[(2-methylpropanoyl)oxy]-2,5-dioxo-dodecahydrocyclodeca[b]furan-11-yl 2-methylpropanoate

> <JCHEM_LOGP>
2.472191308666667

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.93983827500329

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.150598986852046

> <JCHEM_PKA_STRONGEST_BASIC>
-2.7380644005027444

> <JCHEM_POLAR_SURFACE_AREA>
136.43

> <JCHEM_REFRACTIVITY>
111.60539999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(3aR,4S,6S,8S,10S,11S,11aR)-8,10-dihydroxy-6,10-dimethyl-3-methylidene-4-[(2-methylpropanoyl)oxy]-2,5-dioxo-octahydrocyclodeca[b]furan-11-yl 2-methylpropanoate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 09-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   09-SEP-22         0                                  
HETATM    1  C   UNK     0       3.417  -3.528   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.379  -2.326   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       3.972  -0.840   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       2.531  -0.296   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0       5.259   0.006   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       6.461  -0.957   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       7.981  -0.707   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       7.005   0.484   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       7.549   1.925   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       9.719   2.110   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       6.573   3.116   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       7.117   4.557   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.053   2.867   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       8.525   0.734   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       8.328   2.261   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       9.018   2.193   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0      10.044   0.983   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      11.020  -0.208   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      12.540   0.041   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0      10.476  -1.649   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       8.957  -1.898   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       7.467  -1.508   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       8.413  -3.339   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       9.389  -4.531   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0       6.893  -3.589   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       6.350  -5.030   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0       7.325  -6.221   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0       8.845  -5.971   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0       6.782  -7.662   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       7.758  -8.853   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       5.262  -7.911   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       5.917  -2.397   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   32                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6                                                       
CONECT    6    5    7   32                                                  
CONECT    7    6    8   14                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11                                                            
CONECT   14    7   15   16   17                                             
CONECT   15   14                                                            
CONECT   16   14                                                            
CONECT   17   14   18                                                       
CONECT   18   17   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18   21                                                       
CONECT   21   20   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23   26   32                                                  
CONECT   26   25   27                                                       
CONECT   27   26   28   29                                                  
CONECT   28   27                                                            
CONECT   29   27   30   31                                                  
CONECT   30   29                                                            
CONECT   31   29                                                            
CONECT   32   25    2    6                                                  
MASTER        0    0    0    0    0    0    0    0   32    0   66    0
END

View in JSmol

Synonyms

Value	Source
2,10-Dihydroxy-5-oxo-6,9-bis(isobutyloxy)germacran-8,12-olide	ChEBI

Chemical Formula

C₂₃H₃₄O₉

Average Mass

454.5160 Da

Monoisotopic Mass

454.22028 Da

IUPAC Name

(3aR,4S,6S,8S,10S,11S,11aR)-8,10-dihydroxy-6,10-dimethyl-3-methylidene-4-[(2-methylpropanoyl)oxy]-2,5-dioxo-dodecahydrocyclodeca[b]furan-11-yl 2-methylpropanoate

Traditional Name

(3aR,4S,6S,8S,10S,11S,11aR)-8,10-dihydroxy-6,10-dimethyl-3-methylidene-4-[(2-methylpropanoyl)oxy]-2,5-dioxo-octahydrocyclodeca[b]furan-11-yl 2-methylpropanoate

CAS Registry Number

Not Available

SMILES

CC(C)C(=O)O[C@H]1[C@H]2[C@@H](OC(=O)C2=C)[C@H](OC(=O)C(C)C)[C@@](C)(O)C[C@@H](O)C[C@H](C)C1=O

InChI Identifier

InChI=1S/C23H34O9/c1-10(2)20(26)30-17-15-13(6)22(28)31-18(15)19(32-21(27)11(3)4)23(7,29)9-14(24)8-12(5)16(17)25/h10-12,14-15,17-19,24,29H,6,8-9H2,1-5,7H3/t12-,14-,15-,17-,18+,19-,23-/m0/s1

InChI Key

WOJZAWJFEPVGSB-CHYAZBGWSA-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
Carpesium divaricatum	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
Tricarboxylic acid or derivatives
Alpha-acyloxy ketone
Cyclitol or derivatives
Gamma butyrolactone
Enoate ester
Alpha,beta-unsaturated carboxylic ester
Tetrahydrofuran
Tertiary alcohol
Cyclic ketone
Carboxylic acid ester
Secondary alcohol
Ketone
Lactone
Organoheterocyclic compound
Oxacycle
Carboxylic acid derivative
Hydrocarbon derivative
Alcohol
Carbonyl group
Organic oxygen compound
Organic oxide
Organooxygen compound
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

cyclic ketone (CHEBI:65579 )
tertiary alcohol (CHEBI:65579 )
secondary alcohol (CHEBI:65579 )
diol (CHEBI:65579 )
germacranolide (CHEBI:65579 )

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	2.47	ChemAxon
pKa (Strongest Acidic)	13.15	ChemAxon
pKa (Strongest Basic)	-2.7	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	136.43 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	111.61 m³·mol⁻¹	ChemAxon
Polarizability	46.6 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

C00050339

Chemspider ID

10197245

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

21582601

PDB ID

Not Available

ChEBI ID

65579

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for cardivin d (NP0291038)

MOL for NP0291038 (cardivin d)

3D MOL for NP0291038 (cardivin d)

3D SDF for NP0291038 (cardivin d)

3D-SDF for NP0291038 (cardivin d)

PDB for NP0291038 (cardivin d)

3D PDB for NP0291038 (cardivin d)

SMILES for NP0291038 (cardivin d)

INCHI for NP0291038 (cardivin d)

Structure for NP0291038 (cardivin d)

3D Structure for NP0291038 (cardivin d)