NP-MRD: Showing NP-Card for Picroside III (NP0057433)

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Record Information

Version

2.0

Created at

2022-04-28 02:52:16 UTC

Updated at

2022-04-28 02:52:17 UTC

NP-MRD ID

NP0057433

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Picroside III

Description

[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-{[(1S,2S,4S,5S,6R,10S)-5-hydroxy-2-(hydroxymethyl)-3,9-dioxatricyclo[4.4.0.0²,⁴]Dec-7-en-10-yl]oxy}oxan-2-yl]methyl (2E)-3-(4-hydroxy-3-methoxyphenyl)prop-2-enoate belongs to the class of organic compounds known as coumaric acids and derivatives. These are aromatic compounds containing Aromatic compounds containing a cinnamic acid moiety (or a derivative thereof) hydroxylated at the C2 (ortho-), C3 (meta-), or C4 (para-) carbon atom of the benzene ring. Picroside III is found in Neopicrorhiza scrophulariiflora , Picrorhiza kurrooa, Picrorrhiza kurrooa, Scutellaria albida and Scutellaria albida subsp.albida. Based on a literature review very few articles have been published on [(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-{[(1S,2S,4S,5S,6R,10S)-5-hydroxy-2-(hydroxymethyl)-3,9-dioxatricyclo[4.4.0.0²,⁴]Dec-7-en-10-yl]oxy}oxan-2-yl]methyl (2E)-3-(4-hydroxy-3-methoxyphenyl)prop-2-enoate.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282204522D          

 38 42  0  0  1  0            999 V2000
    0.5754   -0.8625    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.0205   -0.2919    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.1758    0.5094    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
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   -1.6606   -0.2415    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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  1  2  1  0  0  0  0
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 15 35  1  0  0  0  0
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 33 38  1  1  0  0  0
M  END

     RDKit          3D

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M  END


  Mrv1652304282204522D          

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  8  9  1  0  0  0  0
  2  9  1  6  0  0  0
  9 10  1  0  0  0  0
  8 10  1  1  0  0  0
  9 11  1  6  0  0  0
 11 12  1  0  0  0  0
  7 13  1  1  0  0  0
  1 14  1  1  0  0  0
 15 14  1  6  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  6  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  2  0  0  0  0
 20 22  1  0  0  0  0
 22 23  2  0  0  0  0
 23 24  1  0  0  0  0
 24 25  2  0  0  0  0
 25 26  1  0  0  0  0
 26 27  2  0  0  0  0
 27 28  1  0  0  0  0
 28 29  2  0  0  0  0
 24 29  1  0  0  0  0
 28 30  1  0  0  0  0
 30 31  1  0  0  0  0
 27 32  1  0  0  0  0
 17 33  1  0  0  0  0
 33 34  1  0  0  0  0
 34 35  1  0  0  0  0
 15 35  1  0  0  0  0
 35 36  1  1  0  0  0
 34 37  1  1  0  0  0
 33 38  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0057433

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=CC(\C=C\C(=O)OC[C@@H]2O[C@H](O[C@@H]3OC=C[C@H]4[C@H](O)[C@@H]5O[C@]5(CO)[C@@H]34)[C@@H](O)[C@@H](O)[C@H]2O)=CC=C1O

> <INCHI_IDENTIFIER>
InChI=1S/C25H30O13/c1-33-14-8-11(2-4-13(14)27)3-5-16(28)35-9-15-19(30)20(31)21(32)24(36-15)37-23-17-12(6-7-34-23)18(29)22-25(17,10-26)38-22/h2-8,12,15,17-24,26-27,29-32H,9-10H2,1H3/b5-3+/t12-,15+,17-,18+,19+,20+,21+,22+,23+,24-,25-/m1/s1

> <INCHI_KEY>
DPHFMUYFANVRJL-KLPNLWAHSA-N

> <FORMULA>
C25H30O13

> <MOLECULAR_WEIGHT>
538.502

> <EXACT_MASS>
538.168641026

> <JCHEM_ACCEPTOR_COUNT>
12

> <JCHEM_ATOM_COUNT>
68

> <JCHEM_AVERAGE_POLARIZABILITY>
52.63740190610004

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-{[(1S,2S,4S,5S,6R,10S)-5-hydroxy-2-(hydroxymethyl)-3,9-dioxatricyclo[4.4.0.0^{2,4}]dec-7-en-10-yl]oxy}oxan-2-yl]methyl (2E)-3-(4-hydroxy-3-methoxyphenyl)prop-2-enoate

> <ALOGPS_LOGP>
-0.05

> <JCHEM_LOGP>
-0.859149479

> <ALOGPS_LOGS>
-2.52

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.194944596098116

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.865741913064829

> <JCHEM_PKA_STRONGEST_BASIC>
-3.1218025089548433

> <JCHEM_POLAR_SURFACE_AREA>
197.13

> <JCHEM_REFRACTIVITY>
125.2033

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.62e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-{[(1S,2S,4S,5S,6R,10S)-5-hydroxy-2-(hydroxymethyl)-3,9-dioxatricyclo[4.4.0.0^{2,4}]dec-7-en-10-yl]oxy}oxan-2-yl]methyl (2E)-3-(4-hydroxy-3-methoxyphenyl)prop-2-enoate

> <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       1.074  -1.610   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.038  -0.545   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.328   0.951   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.807   1.382   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.919   0.316   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       2.553  -1.179   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      -0.981   1.762   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -2.157   0.767   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -1.574  -0.659   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -3.100  -0.451   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0      -1.621  -2.198   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      -2.978  -2.927   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      -1.095   3.297   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       0.708  -3.106   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       1.820  -4.171   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       1.454  -5.667   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       2.566  -6.732   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       2.200  -8.228   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       0.721  -8.658   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       0.355 -10.154   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       1.467 -11.219   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0      -1.124 -10.585   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -1.490 -12.081   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -2.969 -12.511   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -3.335 -14.007   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -4.814 -14.438   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      -5.926 -13.373   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      -5.560 -11.877   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      -4.081 -11.446   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0      -6.672 -10.812   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0      -8.150 -11.242   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0      -7.405 -13.803   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0       4.044  -6.301   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       4.411  -4.805   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       3.299  -3.740   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0       3.665  -2.245   0.000  0.00  0.00           O+0
HETATM   37  O   UNK     0       5.889  -4.375   0.000  0.00  0.00           O+0
HETATM   38  O   UNK     0       5.157  -7.366   0.000  0.00  0.00           O+0
CONECT    1    2    6   14                                                  
CONECT    2    1    3    9                                                  
CONECT    3    2    4    7                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    1                                                       
CONECT    7    3    8   13                                                  
CONECT    8    7    9   10                                                  
CONECT    9    8    2   10   11                                             
CONECT   10    9    8                                                       
CONECT   11    9   12                                                       
CONECT   12   11                                                            
CONECT   13    7                                                            
CONECT   14    1   15                                                       
CONECT   15   14   16   35                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18   33                                                  
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   23                                                       
CONECT   23   22   24                                                       
CONECT   24   23   25   29                                                  
CONECT   25   24   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   28   32                                                  
CONECT   28   27   29   30                                                  
CONECT   29   28   24                                                       
CONECT   30   28   31                                                       
CONECT   31   30                                                            
CONECT   32   27                                                            
CONECT   33   17   34   38                                                  
CONECT   34   33   35   37                                                  
CONECT   35   34   15   36                                                  
CONECT   36   35                                                            
CONECT   37   34                                                            
CONECT   38   33                                                            
MASTER        0    0    0    0    0    0    0    0   38    0   84    0
END

View in JSmol

Synonyms

Value	Source
[(2S,3R,4S,5S,6R)-3,4,5-Trihydroxy-6-{[(1S,2S,4S,5S,6R,10S)-5-hydroxy-2-(hydroxymethyl)-3,9-dioxatricyclo[4.4.0.0,]dec-7-en-10-yl]oxy}oxan-2-yl]methyl (2E)-3-(4-hydroxy-3-methoxyphenyl)prop-2-enoic acid	Generator

Chemical Formula

C₂₅H₃₀O₁₃

Average Mass

538.5020 Da

Monoisotopic Mass

538.16864 Da

IUPAC Name

[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-{[(1S,2S,4S,5S,6R,10S)-5-hydroxy-2-(hydroxymethyl)-3,9-dioxatricyclo[4.4.0.0^{2,4}]dec-7-en-10-yl]oxy}oxan-2-yl]methyl (2E)-3-(4-hydroxy-3-methoxyphenyl)prop-2-enoate

Traditional Name

CAS Registry Number

Not Available

SMILES

COC1=CC(\C=C\C(=O)OC[C@@H]2O[C@H](O[C@@H]3OC=C[C@H]4[C@H](O)[C@@H]5O[C@]5(CO)[C@@H]34)[C@@H](O)[C@@H](O)[C@H]2O)=CC=C1O

InChI Identifier

InChI=1S/C25H30O13/c1-33-14-8-11(2-4-13(14)27)3-5-16(28)35-9-15-19(30)20(31)21(32)24(36-15)37-23-17-12(6-7-34-23)18(29)22-25(17,10-26)38-22/h2-8,12,15,17-24,26-27,29-32H,9-10H2,1H3/b5-3+/t12-,15+,17-,18+,19+,20+,21+,22+,23+,24-,25-/m1/s1

InChI Key

DPHFMUYFANVRJL-KLPNLWAHSA-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
Neopicrorhiza scrophulariiflora	Plant	KNApSAcK
Picrorhiza kurrooa	Plant	KNApSAcK
Picrorrhiza kurrooa	-	KNApSAcK
Scutellaria albida	LOTUS Database	35616633
Scutellaria albida subsp.albida	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as coumaric acids and derivatives. These are aromatic compounds containing Aromatic compounds containing a cinnamic acid moiety (or a derivative thereof) hydroxylated at the C2 (ortho-), C3 (meta-), or C4 (para-) carbon atom of the benzene ring.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Cinnamic acids and derivatives

Sub Class

Hydroxycinnamic acids and derivatives

Direct Parent

Coumaric acids and derivatives

Alternative Parents

Substituents

Cinnamic acid ester
Coumaric acid or derivatives
O-glycosyl compound
Glycosyl compound
Methoxyphenol
Phenoxy compound
Methoxybenzene
Styrene
Phenol ether
Anisole
1-hydroxy-2-unsubstituted benzenoid
Phenol
Fatty acid ester
Alkyl aryl ether
Fatty acyl
Benzenoid
Oxane
Monosaccharide
Monocyclic benzene moiety
Alpha,beta-unsaturated carboxylic ester
Enoate ester
Cyclic alcohol
Secondary alcohol
Carboxylic acid ester
Oxacycle
Organoheterocyclic compound
Polyol
Monocarboxylic acid or derivatives
Ether
Oxirane
Dialkyl ether
Carboxylic acid derivative
Acetal
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
Carbonyl group
Alcohol
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic 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	-0.05	ALOGPS
logP	-0.86	ChemAxon
logS	-2.5	ALOGPS
pKa (Strongest Acidic)	9.87	ChemAxon
pKa (Strongest Basic)	-3.1	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	12	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	197.13 Å²	ChemAxon
Rotatable Bond Count	9	ChemAxon
Refractivity	125.2 m³·mol⁻¹	ChemAxon
Polarizability	52.64 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

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

162983203

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Picroside III (NP0057433)

MOL for NP0057433 (Picroside III)

3D MOL for NP0057433 (Picroside III)

3D SDF for NP0057433 (Picroside III)

3D-SDF for NP0057433 (Picroside III)

PDB for NP0057433 (Picroside III)

3D PDB for NP0057433 (Picroside III)

SMILES for NP0057433 (Picroside III)

INCHI for NP0057433 (Picroside III)

Structure for NP0057433 (Picroside III)

3D Structure for NP0057433 (Picroside III)