NP-MRD: Showing NP-Card for 2-(hydroxymethyl)-10-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,9-dioxatricyclo[4.4.0.0²,⁴]dec-7-en-5-yl 4-hydroxy-3-methoxybenzoate (NP0145573)

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Record Information

Version

2.0

Created at

2022-09-02 00:48:10 UTC

Updated at

2022-09-02 00:48:10 UTC

NP-MRD ID

NP0145573

Secondary Accession Numbers

None

Natural Product Identification

Common Name

2-(hydroxymethyl)-10-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,9-dioxatricyclo[4.4.0.0²,⁴]dec-7-en-5-yl 4-hydroxy-3-methoxybenzoate

Description

Picroside II belongs to the class of organic compounds known as hydrolyzable tannins. These are tannins with a structure characterized by either of the following models. In model 1, the structure contains galloyl units (in some cases, shikimic acid units) that are linked to diverse polyol carbohydrate-, catechin-, or triterpenoid units. In model 2, contains at least two galloyl units C-C coupled to each other, and do not contain a glycosidically linked catechin unit. 2-(hydroxymethyl)-10-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,9-dioxatricyclo[4.4.0.0²,⁴]dec-7-en-5-yl 4-hydroxy-3-methoxybenzoate is found in Picrorhiza kurrooa. 2-(hydroxymethyl)-10-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,9-dioxatricyclo[4.4.0.0²,⁴]dec-7-en-5-yl 4-hydroxy-3-methoxybenzoate was first documented in 2022 (PMID: 35293848). Based on a literature review very few articles have been published on Picroside II (PMID: 34883483).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309022202482D          

 36 40  0  0  1  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652309022202482D          

 36 40  0  0  1  0            999 V2000
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 28 31  1  0  0  0  0
 31 32  1  0  0  0  0
  9 32  1  0  0  0  0
 28 32  1  0  0  0  0
  5 33  2  0  0  0  0
 33 34  1  0  0  0  0
 34 35  2  0  0  0  0
  3 35  1  0  0  0  0
 35 36  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0145573

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=CC(=CC=C1O)C(=O)OC1C2OC2(CO)C2C1C=COC2O[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C23H28O13/c1-31-12-6-9(2-3-11(12)26)20(30)34-18-10-4-5-32-21(14(10)23(8-25)19(18)36-23)35-22-17(29)16(28)15(27)13(7-24)33-22/h2-6,10,13-19,21-22,24-29H,7-8H2,1H3/t10?,13-,14?,15-,16+,17-,18?,19?,21?,22+,23?/m1/s1

> <INCHI_KEY>
AKNILCMFRRDTEY-MRFBWRKESA-N

> <FORMULA>
C23H28O13

> <MOLECULAR_WEIGHT>
512.464

> <EXACT_MASS>
512.152990962

> <JCHEM_ACCEPTOR_COUNT>
12

> <JCHEM_ATOM_COUNT>
64

> <JCHEM_AVERAGE_POLARIZABILITY>
49.93300622550189

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-0.38

> <JCHEM_LOGP>
-1.3977403483333328

> <ALOGPS_LOGS>
-2.02

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.203451275973373

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.987941929167713

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9810847601929344

> <JCHEM_POLAR_SURFACE_AREA>
197.13

> <JCHEM_REFRACTIVITY>
115.45760000000003

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
4.92e+00 g/l

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

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 02-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   02-SEP-22         0                                  
HETATM    1  C   UNK     0       3.244   8.309   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       3.358   6.774   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       4.745   6.104   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.859   4.568   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       6.246   3.899   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.360   2.363   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       7.747   1.694   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       5.087   1.497   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       5.200  -0.039   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       6.510  -0.850   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       7.988  -0.419   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       9.101  -1.484   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       8.734  -2.980   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       7.256  -3.411   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       6.889  -4.906   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       8.002  -5.971   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       9.480  -5.541   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0      10.592  -6.606   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      12.071  -6.175   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      12.437  -4.680   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0      10.226  -8.102   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      11.338  -9.167   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0       8.747  -8.532   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       8.381 -10.028   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0       7.635  -7.467   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       6.157  -7.898   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0       6.143  -2.345   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       4.608  -2.459   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       4.560  -3.998   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0       3.204  -4.727   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0       3.082  -2.251   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0       4.025  -1.034   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       7.519   4.766   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       7.405   6.301   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       6.018   6.971   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0       5.904   8.506   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   35                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   33                                                  
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9                                                       
CONECT    9    8   10   32                                                  
CONECT   10    9   11   27                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15   27                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17   25                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19   21                                                  
CONECT   19   18   20                                                       
CONECT   20   19                                                            
CONECT   21   18   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23   16   26                                                  
CONECT   26   25                                                            
CONECT   27   14   10   28                                                  
CONECT   28   27   29   31   32                                             
CONECT   29   28   30                                                       
CONECT   30   29                                                            
CONECT   31   28   32                                                       
CONECT   32   31    9   28                                                  
CONECT   33    5   34                                                       
CONECT   34   33   35                                                       
CONECT   35   34    3   36                                                  
CONECT   36   35                                                            
MASTER        0    0    0    0    0    0    0    0   36    0   80    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₃H₂₈O₁₃

Average Mass

512.4640 Da

Monoisotopic Mass

512.15299 Da

IUPAC Name

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

Traditional Name

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

CAS Registry Number

Not Available

SMILES

COC1=CC(=CC=C1O)C(=O)OC1C2OC2(CO)C2C1C=COC2O[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O

InChI Identifier

InChI=1S/C23H28O13/c1-31-12-6-9(2-3-11(12)26)20(30)34-18-10-4-5-32-21(14(10)23(8-25)19(18)36-23)35-22-17(29)16(28)15(27)13(7-24)33-22/h2-6,10,13-19,21-22,24-29H,7-8H2,1H3/t10?,13-,14?,15-,16+,17-,18?,19?,21?,22+,23?/m1/s1

InChI Key

AKNILCMFRRDTEY-MRFBWRKESA-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
Picrorhiza kurrooa	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as hydrolyzable tannins. These are tannins with a structure characterized by either of the following models. In model 1, the structure contains galloyl units (in some cases, shikimic acid units) that are linked to diverse polyol carbohydrate-, catechin-, or triterpenoid units. In model 2, contains at least two galloyl units C-C coupled to each other, and do not contain a glycosidically linked catechin unit.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Tannins

Sub Class

Hydrolyzable tannins

Direct Parent

Hydrolyzable tannins

Alternative Parents

Substituents

Hydrolyzable tannin
Hexose monosaccharide
P-hydroxybenzoic acid alkyl ester
P-hydroxybenzoic acid ester
O-glycosyl compound
Glycosyl compound
M-methoxybenzoic acid or derivatives
Methoxyphenol
Benzoate ester
Benzoic acid or derivatives
Phenoxy compound
Phenol ether
Anisole
Methoxybenzene
Benzoyl
1-hydroxy-2-unsubstituted benzenoid
Phenol
Alkyl aryl ether
Oxane
Monosaccharide
Benzenoid
Monocyclic benzene moiety
Secondary alcohol
Carboxylic acid ester
Polyol
Ether
Oxirane
Dialkyl ether
Carboxylic acid derivative
Acetal
Organoheterocyclic compound
Oxacycle
Monocarboxylic acid or derivatives
Primary alcohol
Alcohol
Hydrocarbon derivative
Organic oxide
Organic oxygen compound
Organooxygen compound
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	-0.38	ALOGPS
logP	-1.4	ChemAxon
logS	-2	ALOGPS
pKa (Strongest Acidic)	8.99	ChemAxon
pKa (Strongest Basic)	-3	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	8	ChemAxon
Refractivity	115.46 m³·mol⁻¹	ChemAxon
Polarizability	49.93 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

C00010514

Chemspider ID

8024996

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

9849283

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Yao H, Yan J, Yin L, Chen W: Picroside II alleviates DSS-induced ulcerative colitis by suppressing the production of NLRP3 inflammasomes through NF-kappaB signaling pathway. Immunopharmacol Immunotoxicol. 2022 Jun;44(3):437-446. doi: 10.1080/08923973.2022.2054425. Epub 2022 Mar 23. [PubMed:35293848 ]
Li H, Du W, Yuan Y, Xue J, Li Q, Wang L: The Protective Effect of Picroside II on Isoflurane-Induced Neuronal Injury in Rats via Downregulating miR-195. Neuroimmunomodulation. 2022;29(3):202-210. doi: 10.1159/000519779. Epub 2021 Dec 9. [PubMed:34883483 ]
LOTUS database [Link]

Showing NP-Card for 2-(hydroxymethyl)-10-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,9-dioxatricyclo[4.4.0.0²,⁴]dec-7-en-5-yl 4-hydroxy-3-methoxybenzoate (NP0145573)

MOL for NP0145573 (2-(hydroxymethyl)-10-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,9-dioxatricyclo[4.4.0.0²,⁴]dec-7-en-5-yl 4-hydroxy-3-methoxybenzoate)

3D MOL for NP0145573 (2-(hydroxymethyl)-10-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,9-dioxatricyclo[4.4.0.0²,⁴]dec-7-en-5-yl 4-hydroxy-3-methoxybenzoate)

3D SDF for NP0145573 (2-(hydroxymethyl)-10-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,9-dioxatricyclo[4.4.0.0²,⁴]dec-7-en-5-yl 4-hydroxy-3-methoxybenzoate)

3D-SDF for NP0145573 (2-(hydroxymethyl)-10-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,9-dioxatricyclo[4.4.0.0²,⁴]dec-7-en-5-yl 4-hydroxy-3-methoxybenzoate)

PDB for NP0145573 (2-(hydroxymethyl)-10-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,9-dioxatricyclo[4.4.0.0²,⁴]dec-7-en-5-yl 4-hydroxy-3-methoxybenzoate)

3D PDB for NP0145573 (2-(hydroxymethyl)-10-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,9-dioxatricyclo[4.4.0.0²,⁴]dec-7-en-5-yl 4-hydroxy-3-methoxybenzoate)

SMILES for NP0145573 (2-(hydroxymethyl)-10-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,9-dioxatricyclo[4.4.0.0²,⁴]dec-7-en-5-yl 4-hydroxy-3-methoxybenzoate)

INCHI for NP0145573 (2-(hydroxymethyl)-10-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,9-dioxatricyclo[4.4.0.0²,⁴]dec-7-en-5-yl 4-hydroxy-3-methoxybenzoate)

Structure for NP0145573 (2-(hydroxymethyl)-10-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,9-dioxatricyclo[4.4.0.0²,⁴]dec-7-en-5-yl 4-hydroxy-3-methoxybenzoate)

3D Structure for NP0145573 (2-(hydroxymethyl)-10-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,9-dioxatricyclo[4.4.0.0²,⁴]dec-7-en-5-yl 4-hydroxy-3-methoxybenzoate)