NP-MRD: Showing NP-Card for Physalin B (NP0076972)

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Record Information

Version

2.0

Created at

2022-04-28 22:09:08 UTC

Updated at

2022-04-28 22:09:08 UTC

NP-MRD ID

NP0076972

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Physalin B

Description

Physalin B belongs to the class of organic compounds known as physalins and derivatives. These are steroidal constituents of Physalis plants which possess an unusual 13,14-seco-16,24-cyclo-steroidal ring skeleton (where the bond that is normally present between the 13 and 14 positions in other steroids is broken while a new bond between positions 16 and 24 is formed). Physalin B is found in Physalis franchetii, Physalis alkekeng, Physalis alkekengi var.francheti. , Physalis angulata , Physalis lagascae, Physalis minima , Witheringia coccoloboides and Witheringia solanacea . Physalin B was first documented in 2021 (PMID: 34688463). Based on a literature review a small amount of articles have been published on Physalin B (PMID: 35310660) (PMID: 35155671) (PMID: 34737012) (PMID: 34647944).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304292200092D          

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M  END

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  2 28  1  0  0  0  0
 28 29  1  0  0  0  0
 29 30  2  0  0  0  0
 30 31  1  0  0  0  0
  1 31  1  1  0  0  0
 29 32  1  0  0  0  0
 32 33  1  0  0  0  0
 33 34  2  0  0  0  0
 34 35  1  0  0  0  0
 28 35  1  0  0  0  0
 35 36  2  0  0  0  0
 28 37  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0076972

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@@]12OC(=O)[C@@]3(O)CC[C@H]4[C@@H](CC=C5CC=CC(=O)[C@]45C)[C@@]45O[C@@]13[C@@H](C4=O)[C@]1(C)C[C@H]2OC(=O)[C@@H]1CO5

> <INCHI_IDENTIFIER>
InChI=1S/C28H30O9/c1-23-11-18-25(3)28-19(23)20(30)27(37-28,34-12-16(23)21(31)35-18)15-8-7-13-5-4-6-17(29)24(13,2)14(15)9-10-26(28,33)22(32)36-25/h4,6-7,14-16,18-19,33H,5,8-12H2,1-3H3/t14-,15+,16-,18+,19-,23+,24-,25-,26-,27+,28-/m0/s1

> <INCHI_KEY>
HVTFEHJSUSPQBK-DNJDGUCCSA-N

> <FORMULA>
C28H30O9

> <MOLECULAR_WEIGHT>
510.539

> <EXACT_MASS>
510.188982546

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
67

> <JCHEM_AVERAGE_POLARIZABILITY>
50.0925498554742

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1R,2S,5R,8S,9R,17R,18R,21S,24R,26S,27S)-5-hydroxy-2,9,26-trimethyl-3,19,23,28-tetraoxaoctacyclo[16.9.1.1^{18,27}.0^{1,5}.0^{2,24}.0^{8,17}.0^{9,14}.0^{21,26}]nonacosa-11,14-diene-4,10,22,29-tetrone

> <ALOGPS_LOGP>
2.19

> <JCHEM_LOGP>
2.584920492666666

> <ALOGPS_LOGS>
-2.99

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
8

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
11.53007510149464

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.673880869069533

> <JCHEM_PKA_STRONGEST_BASIC>
-4.082489508666034

> <JCHEM_POLAR_SURFACE_AREA>
125.43

> <JCHEM_REFRACTIVITY>
125.70159999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
5.17e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1R,2S,5R,8S,9R,17R,18R,21S,24R,26S,27S)-5-hydroxy-2,9,26-trimethyl-3,19,23,28-tetraoxaoctacyclo[16.9.1.1^{18,27}.0^{1,5}.0^{2,24}.0^{8,17}.0^{9,14}.0^{21,26}]nonacosa-11,14-diene-4,10,22,29-tetrone

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 29-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   29-APR-22         0                                  
HETATM    1  C   UNK     0       7.076   1.979   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       7.996   3.214   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       7.794   4.752   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       6.583   5.705   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       5.028   5.603   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       3.979   4.449   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       4.125   2.458   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       5.498   1.831   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       5.305   3.292   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       6.350   4.424   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       3.526   3.383   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       2.318   2.592   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       1.287   3.733   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       0.775   4.679   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       2.433   5.368   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       2.784   6.860   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       4.322   7.013   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       5.066   8.362   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       1.259   6.365   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      -0.293   3.247   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       0.263   1.623   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      -0.762   0.475   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0       1.885   1.266   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       3.166   0.221   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0       4.773   0.392   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0       3.541   1.656   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0       5.793   6.939   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0       9.525   3.036   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      10.135   1.621   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       9.216   0.386   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       7.686   0.565   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      11.665   1.443   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      12.584   2.678   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      11.974   4.092   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      10.445   4.271   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0       9.835   5.685   0.000  0.00  0.00           O+0
HETATM   37  C   UNK     0       8.915   4.450   0.000  0.00  0.00           C+0
CONECT    1    2    8   31                                                  
CONECT    2    1    3   28                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6   17   27                                             
CONECT    6    5    7   11   15                                             
CONECT    7    6    8                                                       
CONECT    8    7    1    9   25                                             
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9    6   12                                                  
CONECT   12   11   13   23   26                                             
CONECT   13   12   14                                                       
CONECT   14   13   15   20                                                  
CONECT   15   14    6   16   19                                             
CONECT   16   15   17                                                       
CONECT   17   16    5   18                                                  
CONECT   18   17                                                            
CONECT   19   15                                                            
CONECT   20   14   21                                                       
CONECT   21   20   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21   12   24                                                  
CONECT   24   23   25                                                       
CONECT   25   24    8                                                       
CONECT   26   12                                                            
CONECT   27    5                                                            
CONECT   28    2   29   35   37                                             
CONECT   29   28   30   32                                                  
CONECT   30   29   31                                                       
CONECT   31   30    1                                                       
CONECT   32   29   33                                                       
CONECT   33   32   34                                                       
CONECT   34   33   35                                                       
CONECT   35   34   28   36                                                  
CONECT   36   35                                                            
CONECT   37   28                                                            
MASTER        0    0    0    0    0    0    0    0   37    0   88    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₈H₃₀O₉

Average Mass

510.5390 Da

Monoisotopic Mass

510.18898 Da

IUPAC Name

(1R,2S,5R,8S,9R,17R,18R,21S,24R,26S,27S)-5-hydroxy-2,9,26-trimethyl-3,19,23,28-tetraoxaoctacyclo[16.9.1.1^{18,27}.0^{1,5}.0^{2,24}.0^{8,17}.0^{9,14}.0^{21,26}]nonacosa-11,14-diene-4,10,22,29-tetrone

Traditional Name

(1R,2S,5R,8S,9R,17R,18R,21S,24R,26S,27S)-5-hydroxy-2,9,26-trimethyl-3,19,23,28-tetraoxaoctacyclo[16.9.1.1^{18,27}.0^{1,5}.0^{2,24}.0^{8,17}.0^{9,14}.0^{21,26}]nonacosa-11,14-diene-4,10,22,29-tetrone

CAS Registry Number

Not Available

SMILES

C[C@@]12OC(=O)[C@@]3(O)CC[C@H]4[C@@H](CC=C5CC=CC(=O)[C@]45C)[C@@]45O[C@@]13[C@@H](C4=O)[C@]1(C)C[C@H]2OC(=O)[C@@H]1CO5

InChI Identifier

InChI=1S/C28H30O9/c1-23-11-18-25(3)28-19(23)20(30)27(37-28,34-12-16(23)21(31)35-18)15-8-7-13-5-4-6-17(29)24(13,2)14(15)9-10-26(28,33)22(32)36-25/h4,6-7,14-16,18-19,33H,5,8-12H2,1-3H3/t14-,15+,16-,18+,19-,23+,24-,25-,26-,27+,28-/m0/s1

InChI Key

HVTFEHJSUSPQBK-DNJDGUCCSA-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
Alkekengi officinarum var. franchetii	Plant	KNApSAcK
Physalis alkekeng	Plant	KNApSAcK
Physalis alkekengi var.francheti.	Plant	KNApSAcK
Physalis angulata	Plant	KNApSAcK
Physalis lagascae	LOTUS Database	35616633
Physalis minima	Plant	KNApSAcK
Witheringia coccoloboides	LOTUS Database	35616633
Witheringia solanacea	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as physalins and derivatives. These are steroidal constituents of Physalis plants which possess an unusual 13,14-seco-16,24-cyclo-steroidal ring skeleton (where the bond that is normally present between the 13 and 14 positions in other steroids is broken while a new bond between positions 16 and 24 is formed).

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Steroids and steroid derivatives

Sub Class

Physalins and derivatives

Direct Parent

Physalins and derivatives

Alternative Parents

Substituents

Physalin skeleton
Delta valerolactone
Ketal
Cyclohexenone
Delta_valerolactone
Oxepane
Dicarboxylic acid or derivatives
3-furanone
Gamma butyrolactone
Oxane
Cyclic alcohol
Tetrahydrofuran
Tertiary alcohol
Lactone
Ketone
Carboxylic acid ester
Organoheterocyclic compound
Oxacycle
Acetal
Carboxylic acid derivative
Hydrocarbon derivative
Organic oxide
Organic oxygen compound
Carbonyl group
Organooxygen compound
Alcohol
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	2.19	ALOGPS
logP	2.58	ChemAxon
logS	-3	ALOGPS
pKa (Strongest Acidic)	9.67	ChemAxon
pKa (Strongest Basic)	-4.1	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	125.43 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	125.7 m³·mol⁻¹	ChemAxon
Polarizability	50.09 Å³	ChemAxon
Number of Rings	8	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

C00039999

Chemspider ID

23326867

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

11613161

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Yang J, Tian J, Yang Y, Zhu Y, Li C, Zhang Y: RNAi of Sterol Delta24-Isomerase Implicated Its Involvement in Physalin Biosynthesis in Physalis angulata L. Front Plant Sci. 2022 Mar 4;13:850711. doi: 10.3389/fpls.2022.850711. eCollection 2022. [PubMed:35310660 ]
Abate L, Tadesse MG, Bachheti A, Bachheti RK: Traditional and Phytochemical Bases of Herbs, Shrubs, Climbers, and Trees from Ethiopia for Their Anticancer Response. Biomed Res Int. 2022 Feb 3;2022:1589877. doi: 10.1155/2022/1589877. eCollection 2022. [PubMed:35155671 ]
Zhong R, Xia T, Wang Y, Ding Z, Li W, Chen Y, Peng M, Li C, Zhang H, Shu Z: Physalin B ameliorates inflammatory responses in lipopolysaccharide-induced acute lung injury mice by inhibiting NF-kappaB and NLRP3 via the activation of the PI3K/Akt pathway. J Ethnopharmacol. 2022 Feb 10;284:114777. doi: 10.1016/j.jep.2021.114777. Epub 2021 Nov 1. [PubMed:34737012 ]
Zhang W, Bai SS, Zhang Q, Shi RL, Wang HC, Liu YC, Ni TJ, Wu Y, Yao ZY, Sun Y, Wang MY: Physalin B reduces Abeta secretion through down-regulation of BACE1 expression by activating FoxO1 and inhibiting STAT3 phosphorylation. Chin J Nat Med. 2021 Oct;19(10):732-740. doi: 10.1016/S1875-5364(21)60090-0. [PubMed:34688463 ]
Qiu L, Hu L, Liu X, Li W, Zhang X, Xia H, Zhang C: Physalin B inhibits PDGF-BB-induced VSMC proliferation, migration and phenotypic transformation by activating the Nrf2 pathway. Food Funct. 2021 Nov 1;12(21):10950-10966. doi: 10.1039/d1fo01926k. [PubMed:34647944 ]

Showing NP-Card for Physalin B (NP0076972)

MOL for NP0076972 (Physalin B)

3D MOL for NP0076972 (Physalin B)

3D SDF for NP0076972 (Physalin B)

3D-SDF for NP0076972 (Physalin B)

PDB for NP0076972 (Physalin B)

3D PDB for NP0076972 (Physalin B)

SMILES for NP0076972 (Physalin B)

INCHI for NP0076972 (Physalin B)

Structure for NP0076972 (Physalin B)

3D Structure for NP0076972 (Physalin B)