NP-MRD: Showing NP-Card for (2s,3r,4s,5s,6r)-2-{[(3s,4r,4as)-4-ethenyl-8-oxo-3h,4h,4ah,5h,6h-pyrano[3,4-c]pyran-3-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-3-yl (2e)-3-(4-hydroxyphenyl)prop-2-enoate (NP0177576)

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Record Information

Version

2.0

Created at

2022-09-03 15:26:04 UTC

Updated at

2022-09-03 15:26:04 UTC

NP-MRD ID

NP0177576

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2s,3r,4s,5s,6r)-2-{[(3s,4r,4as)-4-ethenyl-8-oxo-3h,4h,4ah,5h,6h-pyrano[3,4-c]pyran-3-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-3-yl (2e)-3-(4-hydroxyphenyl)prop-2-enoate

Description

Olivieroside B belongs to the class of organic compounds known as coumaric acid esters. These are aromatic compounds containing an ester derivative of coumaric acid. (2s,3r,4s,5s,6r)-2-{[(3s,4r,4as)-4-ethenyl-8-oxo-3h,4h,4ah,5h,6h-pyrano[3,4-c]pyran-3-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-3-yl (2e)-3-(4-hydroxyphenyl)prop-2-enoate is found in Gentiana olivieri. Based on a literature review very few articles have been published on Olivieroside B.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309032217262D          

 36 39  0  0  1  0            999 V2000
    2.1434   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    0.0000   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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M  END

     RDKit          3D

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M  END


  Mrv1652309032217262D          

 36 39  0  0  1  0            999 V2000
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M  END
> <DATABASE_ID>
NP0177576

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC[C@H]1O[C@@H](O[C@@H]2OC=C3[C@@H](CCOC3=O)[C@H]2C=C)[C@H](OC(=O)\C=C\C2=CC=C(O)C=C2)[C@@H](O)[C@@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C25H28O11/c1-2-15-16-9-10-32-23(31)17(16)12-33-24(15)36-25-22(21(30)20(29)18(11-26)34-25)35-19(28)8-5-13-3-6-14(27)7-4-13/h2-8,12,15-16,18,20-22,24-27,29-30H,1,9-11H2/b8-5+/t15-,16+,18-,20-,21+,22-,24+,25+/m1/s1

> <INCHI_KEY>
GHVKFCZLAMJIEW-BFQPHHGRSA-N

> <FORMULA>
C25H28O11

> <MOLECULAR_WEIGHT>
504.488

> <EXACT_MASS>
504.163161722

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
64

> <JCHEM_AVERAGE_POLARIZABILITY>
49.67175352391018

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,3R,4S,5S,6R)-2-{[(3S,4R,4aS)-4-ethenyl-8-oxo-3H,4H,4aH,5H,6H,8H-pyrano[3,4-c]pyran-3-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-3-yl (2E)-3-(4-hydroxyphenyl)prop-2-enoate

> <JCHEM_LOGP>
1.6011306660000004

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.69543739337394

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.398348503975805

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9810854088651357

> <JCHEM_POLAR_SURFACE_AREA>
161.21

> <JCHEM_REFRACTIVITY>
122.99659999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(2S,3R,4S,5S,6R)-2-{[(3S,4R,4aS)-4-ethenyl-8-oxo-3H,4H,4aH,5H,6H-pyrano[3,4-c]pyran-3-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-3-yl (2E)-3-(4-hydroxyphenyl)prop-2-enoate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 03-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-SEP-22         0                                  
HETATM    1  C   UNK     0       4.001  -5.390   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       0.000  -3.080   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       0.000  -4.620   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       1.334  -5.390   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       1.334  -6.930   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.667  -7.700   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       2.667  -9.240   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       0.000  -7.700   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       0.000  -9.240   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      -1.334  -6.930   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      -2.667  -7.700   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0      -1.334  -5.390   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      -2.667  -4.620   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0      -4.001  -5.390   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      -4.001  -6.930   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0      -5.335  -4.620   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -6.668  -5.390   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -8.002  -4.620   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      -9.336  -5.390   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0     -10.669  -4.620   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0     -10.669  -3.080   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0     -12.003  -2.310   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0      -9.336  -2.310   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      -8.002  -3.080   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0       1.334  -0.770   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0       5.335   1.540   0.000  0.00  0.00           O+0
HETATM   33  O   UNK     0       6.668  -0.770   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0       6.668  -2.310   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   36                                                  
CONECT    4    3    5   28                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7   15                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9   11                                                  
CONECT    9    8   10                                                       
CONECT   10    9                                                            
CONECT   11    8   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13    6   16                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   22   27                                                  
CONECT   22   21   23                                                       
CONECT   23   22   24                                                       
CONECT   24   23   25   26                                                  
CONECT   25   24                                                            
CONECT   26   24   27                                                       
CONECT   27   26   21                                                       
CONECT   28    4   29                                                       
CONECT   29   28   30                                                       
CONECT   30   29   31   36                                                  
CONECT   31   30   32   33                                                  
CONECT   32   31                                                            
CONECT   33   31   34                                                       
CONECT   34   33   35                                                       
CONECT   35   34   36                                                       
CONECT   36   35   30    3                                                  
MASTER        0    0    0    0    0    0    0    0   36    0   78    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₅H₂₈O₁₁

Average Mass

504.4880 Da

Monoisotopic Mass

504.16316 Da

IUPAC Name

(2S,3R,4S,5S,6R)-2-{[(3S,4R,4aS)-4-ethenyl-8-oxo-3H,4H,4aH,5H,6H,8H-pyrano[3,4-c]pyran-3-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-3-yl (2E)-3-(4-hydroxyphenyl)prop-2-enoate

Traditional Name

(2S,3R,4S,5S,6R)-2-{[(3S,4R,4aS)-4-ethenyl-8-oxo-3H,4H,4aH,5H,6H-pyrano[3,4-c]pyran-3-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-3-yl (2E)-3-(4-hydroxyphenyl)prop-2-enoate

CAS Registry Number

Not Available

SMILES

OC[C@H]1O[C@@H](O[C@@H]2OC=C3[C@@H](CCOC3=O)[C@H]2C=C)[C@H](OC(=O)\C=C\C2=CC=C(O)C=C2)[C@@H](O)[C@@H]1O

InChI Identifier

InChI=1S/C25H28O11/c1-2-15-16-9-10-32-23(31)17(16)12-33-24(15)36-25-22(21(30)20(29)18(11-26)34-25)35-19(28)8-5-13-3-6-14(27)7-4-13/h2-8,12,15-16,18,20-22,24-27,29-30H,1,9-11H2/b8-5+/t15-,16+,18-,20-,21+,22-,24+,25+/m1/s1

InChI Key

GHVKFCZLAMJIEW-BFQPHHGRSA-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
Gentiana olivieri	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as coumaric acid esters. These are aromatic compounds containing an ester derivative of coumaric acid.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Cinnamic acids and derivatives

Sub Class

Hydroxycinnamic acids and derivatives

Direct Parent

Coumaric acid esters

Alternative Parents

Substituents

Coumaric acid ester
Coumaric acid or derivatives
Hexose monosaccharide
Cinnamic acid ester
Glycosyl compound
O-glycosyl compound
Styrene
1-hydroxy-2-unsubstituted benzenoid
Delta valerolactone
Fatty acid ester
Delta_valerolactone
Phenol
Monocyclic benzene moiety
Dicarboxylic acid or derivatives
Fatty acyl
Monosaccharide
Benzenoid
Oxane
Enoate ester
Vinylogous ester
Alpha,beta-unsaturated carboxylic ester
Secondary alcohol
Lactone
Carboxylic acid ester
Acetal
Organoheterocyclic compound
Carboxylic acid derivative
Oxacycle
Organic oxygen compound
Organooxygen compound
Primary alcohol
Organic oxide
Hydrocarbon derivative
Alcohol
Carbonyl group
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	1.6	ChemAxon
pKa (Strongest Acidic)	9.4	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	161.21 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	123 m³·mol⁻¹	ChemAxon
Polarizability	49.67 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	Yes	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

8704904

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

10529508

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (2s,3r,4s,5s,6r)-2-{[(3s,4r,4as)-4-ethenyl-8-oxo-3h,4h,4ah,5h,6h-pyrano[3,4-c]pyran-3-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-3-yl (2e)-3-(4-hydroxyphenyl)prop-2-enoate (NP0177576)

MOL for NP0177576 ((2s,3r,4s,5s,6r)-2-{[(3s,4r,4as)-4-ethenyl-8-oxo-3h,4h,4ah,5h,6h-pyrano[3,4-c]pyran-3-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-3-yl (2e)-3-(4-hydroxyphenyl)prop-2-enoate)

3D MOL for NP0177576 ((2s,3r,4s,5s,6r)-2-{[(3s,4r,4as)-4-ethenyl-8-oxo-3h,4h,4ah,5h,6h-pyrano[3,4-c]pyran-3-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-3-yl (2e)-3-(4-hydroxyphenyl)prop-2-enoate)

3D SDF for NP0177576 ((2s,3r,4s,5s,6r)-2-{[(3s,4r,4as)-4-ethenyl-8-oxo-3h,4h,4ah,5h,6h-pyrano[3,4-c]pyran-3-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-3-yl (2e)-3-(4-hydroxyphenyl)prop-2-enoate)

3D-SDF for NP0177576 ((2s,3r,4s,5s,6r)-2-{[(3s,4r,4as)-4-ethenyl-8-oxo-3h,4h,4ah,5h,6h-pyrano[3,4-c]pyran-3-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-3-yl (2e)-3-(4-hydroxyphenyl)prop-2-enoate)

PDB for NP0177576 ((2s,3r,4s,5s,6r)-2-{[(3s,4r,4as)-4-ethenyl-8-oxo-3h,4h,4ah,5h,6h-pyrano[3,4-c]pyran-3-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-3-yl (2e)-3-(4-hydroxyphenyl)prop-2-enoate)

3D PDB for NP0177576 ((2s,3r,4s,5s,6r)-2-{[(3s,4r,4as)-4-ethenyl-8-oxo-3h,4h,4ah,5h,6h-pyrano[3,4-c]pyran-3-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-3-yl (2e)-3-(4-hydroxyphenyl)prop-2-enoate)

SMILES for NP0177576 ((2s,3r,4s,5s,6r)-2-{[(3s,4r,4as)-4-ethenyl-8-oxo-3h,4h,4ah,5h,6h-pyrano[3,4-c]pyran-3-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-3-yl (2e)-3-(4-hydroxyphenyl)prop-2-enoate)

INCHI for NP0177576 ((2s,3r,4s,5s,6r)-2-{[(3s,4r,4as)-4-ethenyl-8-oxo-3h,4h,4ah,5h,6h-pyrano[3,4-c]pyran-3-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-3-yl (2e)-3-(4-hydroxyphenyl)prop-2-enoate)

Structure for NP0177576 ((2s,3r,4s,5s,6r)-2-{[(3s,4r,4as)-4-ethenyl-8-oxo-3h,4h,4ah,5h,6h-pyrano[3,4-c]pyran-3-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-3-yl (2e)-3-(4-hydroxyphenyl)prop-2-enoate)

3D Structure for NP0177576 ((2s,3r,4s,5s,6r)-2-{[(3s,4r,4as)-4-ethenyl-8-oxo-3h,4h,4ah,5h,6h-pyrano[3,4-c]pyran-3-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-3-yl (2e)-3-(4-hydroxyphenyl)prop-2-enoate)