NP-MRD: Showing NP-Card for (+)-Periplocymarin (NP0073657)

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Record Information

Version

2.0

Created at

2022-04-28 18:53:04 UTC

Updated at

2022-04-28 18:53:04 UTC

NP-MRD ID

NP0073657

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(+)-Periplocymarin

Description

Periplocymarin belongs to the class of organic compounds known as cardenolide glycosides and derivatives. Cardenolide glycosides and derivatives are compounds containing a carbohydrate glycosidically bound to the cardenolide moiety. (+)-Periplocymarin is found in Periploca forrestii, Periploca forrestii Schltr., Periploca graeca, Periploca sepium , Periploca sepium Bge. , Strophanthus eminii, Strophanthus hispidus, Strophanthus kombe and Strophanthus nicholsonii. (+)-Periplocymarin was first documented in 2021 (PMID: 34900704). Based on a literature review a small amount of articles have been published on Periplocymarin (PMID: 35478323) (PMID: 34816469) (PMID: 35365949) (PMID: 34869633).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282220532D          

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M  END

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M  END


  Mrv1652304282220532D          

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   -0.6582   -1.2846    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9385   -2.0605    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.7507   -2.2057    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.2825   -1.5750    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.0022   -0.7991    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0946   -1.7202    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3749   -2.4961    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0310   -2.9816    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4067   -2.6912    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9660   -0.9941    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8069    1.3336    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4850   -0.5835    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3228    1.7357    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  2  0  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  1  6  1  0  0  0  0
  7  1  1  1  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
  7 11  1  0  0  0  0
  9 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  1  0  0  0
 14 15  1  0  0  0  0
  8 15  1  0  0  0  0
 13 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 12 19  1  6  0  0  0
 17 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 16 23  1  0  0  0  0
 21 24  1  1  0  0  0
 25 24  1  6  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 27 28  1  0  0  0  0
 28 29  1  0  0  0  0
 29 30  1  0  0  0  0
 25 30  1  0  0  0  0
 29 31  1  1  0  0  0
 31 32  1  0  0  0  0
 28 33  1  1  0  0  0
 27 34  1  6  0  0  0
 17 35  1  1  0  0  0
 16 36  1  1  0  0  0
  9 37  1  1  0  0  0
  8 38  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0073657

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CO[C@H]1C[C@H](O[C@H]2CC[C@]3(C)[C@H]4CC[C@]5(C)[C@H](CC[C@]5(O)[C@@H]4CC[C@]3(O)C2)C2=CC(=O)OC2)O[C@H](C)[C@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C30H46O8/c1-17-26(32)23(35-4)14-25(37-17)38-19-5-9-27(2)21-6-10-28(3)20(18-13-24(31)36-16-18)8-12-30(28,34)22(21)7-11-29(27,33)15-19/h13,17,19-23,25-26,32-34H,5-12,14-16H2,1-4H3/t17-,19+,20-,21+,22-,23+,25+,26-,27-,28-,29+,30+/m1/s1

> <INCHI_KEY>
XRWQBDJPMXRDOQ-YUUDFPFBSA-N

> <FORMULA>
C30H46O8

> <MOLECULAR_WEIGHT>
534.69

> <EXACT_MASS>
534.319268441

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
84

> <JCHEM_AVERAGE_POLARIZABILITY>
58.70248980646467

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
4-[(1S,2R,5S,7S,10R,11S,14R,15R)-7,11-dihydroxy-5-{[(2R,4S,5R,6R)-5-hydroxy-4-methoxy-6-methyloxan-2-yl]oxy}-2,15-dimethyltetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadecan-14-yl]-2,5-dihydrofuran-2-one

> <ALOGPS_LOGP>
1.57

> <JCHEM_LOGP>
2.655099703666666

> <ALOGPS_LOGS>
-4.67

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.178919787259716

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.182635783394328

> <JCHEM_PKA_STRONGEST_BASIC>
0.2421969716431681

> <JCHEM_POLAR_SURFACE_AREA>
114.68000000000002

> <JCHEM_REFRACTIVITY>
139.2352

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.15e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
4-[(1S,2R,5S,7S,10R,11S,14R,15R)-7,11-dihydroxy-5-{[(2R,4S,5R,6R)-5-hydroxy-4-methoxy-6-methyloxan-2-yl]oxy}-2,15-dimethyltetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadecan-14-yl]-5H-furan-2-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  C   UNK     0       9.882   3.020   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       9.454   4.499   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      10.728   5.364   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      10.779   6.903   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0      11.944   4.418   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      11.421   2.970   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       8.937   1.804   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       7.398   1.854   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       6.874   0.406   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       8.090  -0.539   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       9.365   0.325   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       5.358   0.135   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       4.366   1.312   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.889   2.761   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       6.405   3.032   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       2.850   1.041   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       2.326  -0.407   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       3.319  -1.585   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       4.835  -1.314   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       0.810  -0.678   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -0.182   0.499   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       0.341   1.947   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       1.857   2.218   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0      -1.698   0.228   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0      -2.221  -1.221   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0      -1.229  -2.398   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0      -1.752  -3.846   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      -3.268  -4.117   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      -4.261  -2.940   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      -3.737  -1.492   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0      -5.777  -3.211   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0      -6.300  -4.659   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0      -3.791  -5.566   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0      -0.759  -5.024   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0       1.803  -1.856   0.000  0.00  0.00           O+0
HETATM   36  C   UNK     0       3.373   2.489   0.000  0.00  0.00           C+0
HETATM   37  O   UNK     0       6.505  -1.089   0.000  0.00  0.00           O+0
HETATM   38  C   UNK     0       8.069   3.240   0.000  0.00  0.00           C+0
CONECT    1    2    6    7                                                  
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6                                                       
CONECT    6    5    1                                                       
CONECT    7    1    8   11                                                  
CONECT    8    7    9   15   38                                             
CONECT    9    8   10   12   37                                             
CONECT   10    9   11                                                       
CONECT   11   10    7                                                       
CONECT   12    9   13   19                                                  
CONECT   13   12   14   16                                                  
CONECT   14   13   15                                                       
CONECT   15   14    8                                                       
CONECT   16   13   17   23   36                                             
CONECT   17   16   18   20   35                                             
CONECT   18   17   19                                                       
CONECT   19   18   12                                                       
CONECT   20   17   21                                                       
CONECT   21   20   22   24                                                  
CONECT   22   21   23                                                       
CONECT   23   22   16                                                       
CONECT   24   21   25                                                       
CONECT   25   24   26   30                                                  
CONECT   26   25   27                                                       
CONECT   27   26   28   34                                                  
CONECT   28   27   29   33                                                  
CONECT   29   28   30   31                                                  
CONECT   30   29   25                                                       
CONECT   31   29   32                                                       
CONECT   32   31                                                            
CONECT   33   28                                                            
CONECT   34   27                                                            
CONECT   35   17                                                            
CONECT   36   16                                                            
CONECT   37    9                                                            
CONECT   38    8                                                            
MASTER        0    0    0    0    0    0    0    0   38    0   86    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₃₀H₄₆O₈

Average Mass

534.6900 Da

Monoisotopic Mass

534.31927 Da

IUPAC Name

4-[(1S,2R,5S,7S,10R,11S,14R,15R)-7,11-dihydroxy-5-{[(2R,4S,5R,6R)-5-hydroxy-4-methoxy-6-methyloxan-2-yl]oxy}-2,15-dimethyltetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadecan-14-yl]-2,5-dihydrofuran-2-one

Traditional Name

4-[(1S,2R,5S,7S,10R,11S,14R,15R)-7,11-dihydroxy-5-{[(2R,4S,5R,6R)-5-hydroxy-4-methoxy-6-methyloxan-2-yl]oxy}-2,15-dimethyltetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadecan-14-yl]-5H-furan-2-one

CAS Registry Number

Not Available

SMILES

CO[C@H]1C[C@H](O[C@H]2CC[C@]3(C)[C@H]4CC[C@]5(C)[C@H](CC[C@]5(O)[C@@H]4CC[C@]3(O)C2)C2=CC(=O)OC2)O[C@H](C)[C@H]1O

InChI Identifier

InChI=1S/C30H46O8/c1-17-26(32)23(35-4)14-25(37-17)38-19-5-9-27(2)21-6-10-28(3)20(18-13-24(31)36-16-18)8-12-30(28,34)22(21)7-11-29(27,33)15-19/h13,17,19-23,25-26,32-34H,5-12,14-16H2,1-4H3/t17-,19+,20-,21+,22-,23+,25+,26-,27-,28-,29+,30+/m1/s1

InChI Key

XRWQBDJPMXRDOQ-YUUDFPFBSA-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, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, 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
Periploca forrestii	LOTUS Database	35616633
Periploca forrestii Schltr.	Plant	KNApSAcK
Periploca graeca	LOTUS Database	35616633
Periploca sepium	Plant	KNApSAcK
Periploca sepium BGE.	Plant	KNApSAcK
Strophanthus eminii	LOTUS Database	35616633
Strophanthus hispidus	LOTUS Database	35616633
Strophanthus kombe	LOTUS Database	35616633
Strophanthus nicholsonii	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as cardenolide glycosides and derivatives. Cardenolide glycosides and derivatives are compounds containing a carbohydrate glycosidically bound to the cardenolide moiety.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Steroids and steroid derivatives

Sub Class

Steroid lactones

Direct Parent

Cardenolide glycosides and derivatives

Alternative Parents

Substituents

Cardanolide-glycoside
Steroidal glycoside
14-hydroxysteroid
5-hydroxysteroid
Hydroxysteroid
Hexose monosaccharide
Glycosyl compound
O-glycosyl compound
2-furanone
Monosaccharide
Oxane
Tertiary alcohol
Cyclic alcohol
Enoate ester
Alpha,beta-unsaturated carboxylic ester
Dihydrofuran
Lactone
Carboxylic acid ester
Secondary alcohol
Organoheterocyclic compound
Monocarboxylic acid or derivatives
Carboxylic acid derivative
Acetal
Ether
Dialkyl ether
Oxacycle
Hydrocarbon derivative
Organic oxygen compound
Alcohol
Carbonyl group
Organooxygen compound
Organic oxide
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	1.57	ALOGPS
logP	2.66	ChemAxon
logS	-4.7	ALOGPS
pKa (Strongest Acidic)	7.18	ChemAxon
pKa (Strongest Basic)	0.24	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	114.68 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	139.24 m³·mol⁻¹	ChemAxon
Polarizability	58.7 Å³	ChemAxon
Number of Rings	6	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	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

C00034117

Chemspider ID

10223840

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

12305974

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Tang XY, Dai ZQ, Zeng JX, Li ZT, Fan CL, Yao ZH, Yao XS, Dai Y: Pharmacokinetics, hepatic disposition, and heart tissue distribution of 14 compounds in rat after oral administration of Qi-Li-Qiang-Xin capsule via ultra-high-performance liquid chromatography coupled with triple quadrupole tandem mass spectrometry. J Sep Sci. 2022 Apr 28. doi: 10.1002/jssc.202101008. [PubMed:35478323 ]
Wang S, Yu X, Wu S, Yang W, Gao Y, Wang W, Wang Q, Wei M, Zhu M, Wu J, Yuan Z, Li Y: Simultaneous determination of periplocin, periplocymarin, periplogenin, periplocoside M and periplocoside N of Cortex Periplocae in rat plasma and its application to a pharmacokinetic study. Biomed Chromatogr. 2022 Mar;36(3):e5283. doi: 10.1002/bmc.5283. Epub 2021 Dec 8. [PubMed:34816469 ]
Fan CL, Liang S, Ye MN, Cai WJ, Chen M, Hou YL, Guo J, Dai Y: Periplocymarin alleviates pathological cardiac hypertrophy via inhibiting the JAK2/STAT3 signalling pathway. J Cell Mol Med. 2022 May;26(9):2607-2619. doi: 10.1111/jcmm.17267. Epub 2022 Apr 1. [PubMed:35365949 ]
Cheng Y, Wang G, Zhao L, Dai S, Han J, Hu X, Zhou C, Wang F, Ma H, Li B, Meng Z: Periplocymarin Induced Colorectal Cancer Cells Apoptosis Via Impairing PI3K/AKT Pathway. Front Oncol. 2021 Nov 25;11:753598. doi: 10.3389/fonc.2021.753598. eCollection 2021. [PubMed:34900704 ]
Yun W, Qian L, Yuan R, Xu H: Periplocymarin Alleviates Doxorubicin-Induced Heart Failure and Excessive Accumulation of Ceramides. Front Cardiovasc Med. 2021 Nov 19;8:732554. doi: 10.3389/fcvm.2021.732554. eCollection 2021. [PubMed:34869633 ]

Showing NP-Card for (+)-Periplocymarin (NP0073657)

MOL for NP0073657 ((+)-Periplocymarin)

3D MOL for NP0073657 ((+)-Periplocymarin)

3D SDF for NP0073657 ((+)-Periplocymarin)

3D-SDF for NP0073657 ((+)-Periplocymarin)

PDB for NP0073657 ((+)-Periplocymarin)

3D PDB for NP0073657 ((+)-Periplocymarin)

SMILES for NP0073657 ((+)-Periplocymarin)

INCHI for NP0073657 ((+)-Periplocymarin)

Structure for NP0073657 ((+)-Periplocymarin)

3D Structure for NP0073657 ((+)-Periplocymarin)