NP-MRD: Showing NP-Card for [(2r,3s,4s,5r,6s)-3,4,5-trihydroxy-6-[2-hydroxy-4-(3-oxobutyl)phenoxy]oxan-2-yl]methyl (2z)-3-(3,4-dihydroxyphenyl)prop-2-enoate (NP0217220)

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Record Information

Version

2.0

Created at

2022-09-05 17:29:54 UTC

Updated at

2022-09-05 17:29:55 UTC

NP-MRD ID

NP0217220

Secondary Accession Numbers

None

Natural Product Identification

Common Name

[(2r,3s,4s,5r,6s)-3,4,5-trihydroxy-6-[2-hydroxy-4-(3-oxobutyl)phenoxy]oxan-2-yl]methyl (2z)-3-(3,4-dihydroxyphenyl)prop-2-enoate

Description

Vitexfolin B belongs to the class of organic compounds known as phenolic glycosides. These are organic compounds containing a phenolic structure attached to a glycosyl moiety. Some examples of phenolic structures include lignans, and flavonoids. Among the sugar units found in natural glycosides are D-glucose, L-Fructose, and L rhamnose. [(2r,3s,4s,5r,6s)-3,4,5-trihydroxy-6-[2-hydroxy-4-(3-oxobutyl)phenoxy]oxan-2-yl]methyl (2z)-3-(3,4-dihydroxyphenyl)prop-2-enoate is found in Vitex trifolia. Based on a literature review very few articles have been published on Vitexfolin B.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309052219292D          

 36 38  0  0  1  0            999 V2000
    7.8592   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1447   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.1447   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    5.7158   -6.6000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
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    5.0013   -6.1875    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.0013   -5.3625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.1447   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8592   -5.3625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.1447   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
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  6 36  1  0  0  0  0
M  END

     RDKit          3D

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M  END


  Mrv1652309052219292D          

 36 38  0  0  1  0            999 V2000
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M  END
> <DATABASE_ID>
NP0217220

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(=O)CCC1=CC=C(O[C@@H]2O[C@H](COC(=O)\C=C/C3=CC=C(O)C(O)=C3)[C@@H](O)[C@H](O)[C@H]2O)C(O)=C1

> <INCHI_IDENTIFIER>
InChI=1S/C25H28O11/c1-13(26)2-3-14-5-8-19(18(29)11-14)35-25-24(33)23(32)22(31)20(36-25)12-34-21(30)9-6-15-4-7-16(27)17(28)10-15/h4-11,20,22-25,27-29,31-33H,2-3,12H2,1H3/b9-6-/t20-,22-,23+,24-,25-/m1/s1

> <INCHI_KEY>
BNHNQADMJDCLQA-LJKZKEMPSA-N

> <FORMULA>
C25H28O11

> <MOLECULAR_WEIGHT>
504.488

> <EXACT_MASS>
504.163161722

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
64

> <JCHEM_AVERAGE_POLARIZABILITY>
50.56840403147605

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[(2R,3S,4S,5R,6S)-3,4,5-trihydroxy-6-[2-hydroxy-4-(3-oxobutyl)phenoxy]oxan-2-yl]methyl (2Z)-3-(3,4-dihydroxyphenyl)prop-2-enoate

> <JCHEM_LOGP>
1.9367496310000005

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
9.855717993195357

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.09802260216073

> <JCHEM_PKA_STRONGEST_BASIC>
-3.64911030973359

> <JCHEM_POLAR_SURFACE_AREA>
183.20999999999998

> <JCHEM_REFRACTIVITY>
125.15340000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
10

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
[(2R,3S,4S,5R,6S)-3,4,5-trihydroxy-6-[2-hydroxy-4-(3-oxobutyl)phenoxy]oxan-2-yl]methyl (2Z)-3-(3,4-dihydroxyphenyl)prop-2-enoate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 05-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   05-SEP-22         0                                  
HETATM    1  C   UNK     0      14.670  -2.310   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      13.337  -3.080   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      12.003  -2.310   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      13.337  -4.620   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      12.003  -5.390   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      12.003  -6.930   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      10.669  -7.700   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      10.669  -9.240   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      12.003 -10.010   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      12.003 -11.550   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0      10.669 -12.320   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      10.669 -13.860   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       9.336 -14.630   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       9.336 -16.170   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      10.669 -16.940   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      10.669 -18.480   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       9.336 -19.250   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0      12.003 -19.250   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      12.003 -20.790   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      10.669 -21.560   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      10.669 -23.100   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       9.336 -23.870   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       8.002 -23.100   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       6.668 -23.870   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0       8.002 -21.560   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       6.668 -20.790   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0       9.336 -20.790   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       8.002 -13.860   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0       6.668 -14.630   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0       8.002 -12.320   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0       6.668 -11.550   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0       9.336 -11.550   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0       9.336 -10.010   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0      13.337  -9.240   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0      14.670 -10.010   0.000  0.00  0.00           O+0
HETATM   36  C   UNK     0      13.337  -7.700   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7   36                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   34                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12   32                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14   28                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17   18                                                  
CONECT   17   16                                                            
CONECT   18   16   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21   27                                                  
CONECT   21   20   22                                                       
CONECT   22   21   23                                                       
CONECT   23   22   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23   26   27                                                  
CONECT   26   25                                                            
CONECT   27   25   20                                                       
CONECT   28   13   29   30                                                  
CONECT   29   28                                                            
CONECT   30   28   31   32                                                  
CONECT   31   30                                                            
CONECT   32   30   11   33                                                  
CONECT   33   32                                                            
CONECT   34    9   35   36                                                  
CONECT   35   34                                                            
CONECT   36   34    6                                                       
MASTER        0    0    0    0    0    0    0    0   36    0   76    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₅H₂₈O₁₁

Average Mass

504.4880 Da

Monoisotopic Mass

504.16316 Da

IUPAC Name

[(2R,3S,4S,5R,6S)-3,4,5-trihydroxy-6-[2-hydroxy-4-(3-oxobutyl)phenoxy]oxan-2-yl]methyl (2Z)-3-(3,4-dihydroxyphenyl)prop-2-enoate

Traditional Name

[(2R,3S,4S,5R,6S)-3,4,5-trihydroxy-6-[2-hydroxy-4-(3-oxobutyl)phenoxy]oxan-2-yl]methyl (2Z)-3-(3,4-dihydroxyphenyl)prop-2-enoate

CAS Registry Number

Not Available

SMILES

CC(=O)CCC1=CC=C(O[C@@H]2O[C@H](COC(=O)\C=C/C3=CC=C(O)C(O)=C3)[C@@H](O)[C@H](O)[C@H]2O)C(O)=C1

InChI Identifier

InChI=1S/C25H28O11/c1-13(26)2-3-14-5-8-19(18(29)11-14)35-25-24(33)23(32)22(31)20(36-25)12-34-21(30)9-6-15-4-7-16(27)17(28)10-15/h4-11,20,22-25,27-29,31-33H,2-3,12H2,1H3/b9-6-/t20-,22-,23+,24-,25-/m1/s1

InChI Key

BNHNQADMJDCLQA-LJKZKEMPSA-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
Vitex trifolia	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as phenolic glycosides. These are organic compounds containing a phenolic structure attached to a glycosyl moiety. Some examples of phenolic structures include lignans, and flavonoids. Among the sugar units found in natural glycosides are D-glucose, L-Fructose, and L rhamnose.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Phenolic glycosides

Alternative Parents

Substituents

Fatty acyl glycoside
Phenolic glycoside
Fatty acyl glycoside of mono- or disaccharide
Alkyl glycoside
Cinnamic acid or derivatives
Coumaric acid or derivatives
Hydroxycinnamic acid or derivatives
Cinnamic acid ester
O-glycosyl compound
Phenoxy compound
Catechol
Phenol ether
Styrene
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Fatty acid ester
Phenol
Monocyclic benzene moiety
Monosaccharide
Fatty acyl
Oxane
Benzenoid
Alpha,beta-unsaturated carboxylic ester
Enoate ester
Ketone
Secondary alcohol
Carboxylic acid ester
Oxacycle
Polyol
Monocarboxylic acid or derivatives
Carboxylic acid derivative
Organoheterocyclic compound
Acetal
Aldehyde
Carbonyl group
Alcohol
Organic oxide
Hydrocarbon derivative
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic 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	1.94	ChemAxon
pKa (Strongest Acidic)	9.1	ChemAxon
pKa (Strongest Basic)	-3.6	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	183.21 Å²	ChemAxon
Rotatable Bond Count	10	ChemAxon
Refractivity	125.15 m³·mol⁻¹	ChemAxon
Polarizability	50.57 Å³	ChemAxon
Number of Rings	3	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

101945298

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for [(2r,3s,4s,5r,6s)-3,4,5-trihydroxy-6-[2-hydroxy-4-(3-oxobutyl)phenoxy]oxan-2-yl]methyl (2z)-3-(3,4-dihydroxyphenyl)prop-2-enoate (NP0217220)

MOL for NP0217220 ([(2r,3s,4s,5r,6s)-3,4,5-trihydroxy-6-[2-hydroxy-4-(3-oxobutyl)phenoxy]oxan-2-yl]methyl (2z)-3-(3,4-dihydroxyphenyl)prop-2-enoate)

3D MOL for NP0217220 ([(2r,3s,4s,5r,6s)-3,4,5-trihydroxy-6-[2-hydroxy-4-(3-oxobutyl)phenoxy]oxan-2-yl]methyl (2z)-3-(3,4-dihydroxyphenyl)prop-2-enoate)

3D SDF for NP0217220 ([(2r,3s,4s,5r,6s)-3,4,5-trihydroxy-6-[2-hydroxy-4-(3-oxobutyl)phenoxy]oxan-2-yl]methyl (2z)-3-(3,4-dihydroxyphenyl)prop-2-enoate)

3D-SDF for NP0217220 ([(2r,3s,4s,5r,6s)-3,4,5-trihydroxy-6-[2-hydroxy-4-(3-oxobutyl)phenoxy]oxan-2-yl]methyl (2z)-3-(3,4-dihydroxyphenyl)prop-2-enoate)

PDB for NP0217220 ([(2r,3s,4s,5r,6s)-3,4,5-trihydroxy-6-[2-hydroxy-4-(3-oxobutyl)phenoxy]oxan-2-yl]methyl (2z)-3-(3,4-dihydroxyphenyl)prop-2-enoate)

3D PDB for NP0217220 ([(2r,3s,4s,5r,6s)-3,4,5-trihydroxy-6-[2-hydroxy-4-(3-oxobutyl)phenoxy]oxan-2-yl]methyl (2z)-3-(3,4-dihydroxyphenyl)prop-2-enoate)

SMILES for NP0217220 ([(2r,3s,4s,5r,6s)-3,4,5-trihydroxy-6-[2-hydroxy-4-(3-oxobutyl)phenoxy]oxan-2-yl]methyl (2z)-3-(3,4-dihydroxyphenyl)prop-2-enoate)

INCHI for NP0217220 ([(2r,3s,4s,5r,6s)-3,4,5-trihydroxy-6-[2-hydroxy-4-(3-oxobutyl)phenoxy]oxan-2-yl]methyl (2z)-3-(3,4-dihydroxyphenyl)prop-2-enoate)

Structure for NP0217220 ([(2r,3s,4s,5r,6s)-3,4,5-trihydroxy-6-[2-hydroxy-4-(3-oxobutyl)phenoxy]oxan-2-yl]methyl (2z)-3-(3,4-dihydroxyphenyl)prop-2-enoate)

3D Structure for NP0217220 ([(2r,3s,4s,5r,6s)-3,4,5-trihydroxy-6-[2-hydroxy-4-(3-oxobutyl)phenoxy]oxan-2-yl]methyl (2z)-3-(3,4-dihydroxyphenyl)prop-2-enoate)