NP-MRD: Showing NP-Card for [(2r,3r)-3-(4-hydroxy-3,5-dimethoxyphenyl)-5-methoxy-9-oxo-2h,3h-[1,4]dioxino[2,3-h]chromen-2-yl]methyl 3,4-dihydroxybenzoate (NP0249046)

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Record Information

Version

2.0

Created at

2022-09-07 11:30:03 UTC

Updated at

2022-09-07 11:30:03 UTC

NP-MRD ID

NP0249046

Secondary Accession Numbers

None

Natural Product Identification

Common Name

[(2r,3r)-3-(4-hydroxy-3,5-dimethoxyphenyl)-5-methoxy-9-oxo-2h,3h-[1,4]dioxino[2,3-h]chromen-2-yl]methyl 3,4-dihydroxybenzoate

Description

Repenin D belongs to the class of organic compounds known as coumarinolignans. These are lignans with a structure characterized by the presence of a 1,4-dioxane bridge substituted by a phenyl group, and fused to a coumarin. [(2r,3r)-3-(4-hydroxy-3,5-dimethoxyphenyl)-5-methoxy-9-oxo-2h,3h-[1,4]dioxino[2,3-h]chromen-2-yl]methyl 3,4-dihydroxybenzoate is found in Duranta erecta. Based on a literature review very few articles have been published on Repenin D.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309072213302D          

 40 44  0  0  1  0            999 V2000
   -0.0296    1.3184    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4421    0.6039    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


  Mrv1652309072213302D          

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 16 18  1  0  0  0  0
 18 19  1  0  0  0  0
 13 19  1  0  0  0  0
 19 20  2  0  0  0  0
  8 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
  6 22  1  0  0  0  0
 22 23  1  6  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  2  0  0  0  0
 25 27  1  0  0  0  0
 27 28  2  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
 30 32  1  0  0  0  0
 32 33  1  0  0  0  0
 32 34  2  0  0  0  0
 27 34  1  0  0  0  0
  5 35  2  0  0  0  0
 35 36  1  0  0  0  0
 36 37  1  0  0  0  0
 37 38  1  0  0  0  0
 36 39  2  0  0  0  0
  3 39  1  0  0  0  0
 39 40  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0249046

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=CC(=CC(OC)=C1O)[C@H]1OC2=C(OC)C=C3C=CC(=O)OC3=C2O[C@@H]1COC(=O)C1=CC=C(O)C(O)=C1

> <INCHI_IDENTIFIER>
InChI=1S/C28H24O12/c1-34-18-10-15(11-19(35-2)23(18)32)24-21(12-37-28(33)14-4-6-16(29)17(30)8-14)38-27-25-13(5-7-22(31)39-25)9-20(36-3)26(27)40-24/h4-11,21,24,29-30,32H,12H2,1-3H3/t21-,24-/m1/s1

> <INCHI_KEY>
WQIZCXIRVAHPRD-ZJSXRUAMSA-N

> <FORMULA>
C28H24O12

> <MOLECULAR_WEIGHT>
552.488

> <EXACT_MASS>
552.126776213

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
64

> <JCHEM_AVERAGE_POLARIZABILITY>
54.61272994688898

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[(2R,3R)-3-(4-hydroxy-3,5-dimethoxyphenyl)-5-methoxy-9-oxo-2H,3H,9H-[1,4]dioxino[2,3-h]chromen-2-yl]methyl 3,4-dihydroxybenzoate

> <JCHEM_LOGP>
3.561987472666667

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
9.372025296883555

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.486624694938614

> <JCHEM_PKA_STRONGEST_BASIC>
-4.254739715470029

> <JCHEM_POLAR_SURFACE_AREA>
159.44

> <JCHEM_REFRACTIVITY>
137.9056

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
[(2R,3R)-3-(4-hydroxy-3,5-dimethoxyphenyl)-5-methoxy-9-oxo-2H,3H-[1,4]dioxino[2,3-h]chromen-2-yl]methyl 3,4-dihydroxybenzoate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 07-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   07-SEP-22         0                                  
HETATM    1  C   UNK     0      -0.055   2.461   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0      -0.825   1.127   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0      -0.055  -0.206   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.485  -0.206   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.255  -1.540   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       3.795  -1.540   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       4.565  -0.206   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       6.105  -0.206   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       6.875   1.127   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       6.105   2.461   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       6.875   3.795   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       8.415   1.127   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       9.185  -0.206   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      10.725  -0.206   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      11.495  -1.540   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      10.725  -2.874   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0      11.495  -4.207   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       9.185  -2.874   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       8.415  -1.540   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       6.875  -1.540   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       6.105  -2.874   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       4.565  -2.874   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       3.795  -4.207   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       2.255  -4.207   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0       1.485  -5.541   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0      -0.055  -5.541   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0       2.255  -6.875   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       3.795  -6.875   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       4.565  -8.208   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       3.795  -9.542   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0       4.565 -10.876   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0       2.255  -9.542   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0       1.485 -10.876   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0       1.485  -8.208   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       1.485  -2.874   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      -0.055  -2.874   0.000  0.00  0.00           C+0
HETATM   37  O   UNK     0      -0.825  -4.207   0.000  0.00  0.00           O+0
HETATM   38  C   UNK     0      -2.365  -4.207   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0      -0.825  -1.540   0.000  0.00  0.00           C+0
HETATM   40  O   UNK     0      -2.365  -1.540   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   39                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   35                                                  
CONECT    6    5    7   22                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9   20                                                  
CONECT    9    8   10   12                                                  
CONECT   10    9   11                                                       
CONECT   11   10                                                            
CONECT   12    9   13                                                       
CONECT   13   12   14   19                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17   18                                                  
CONECT   17   16                                                            
CONECT   18   16   19                                                       
CONECT   19   18   13   20                                                  
CONECT   20   19    8   21                                                  
CONECT   21   20   22                                                       
CONECT   22   21    6   23                                                  
CONECT   23   22   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24   26   27                                                  
CONECT   26   25                                                            
CONECT   27   25   28   34                                                  
CONECT   28   27   29                                                       
CONECT   29   28   30                                                       
CONECT   30   29   31   32                                                  
CONECT   31   30                                                            
CONECT   32   30   33   34                                                  
CONECT   33   32                                                            
CONECT   34   32   27                                                       
CONECT   35    5   36                                                       
CONECT   36   35   37   39                                                  
CONECT   37   36   38                                                       
CONECT   38   37                                                            
CONECT   39   36    3   40                                                  
CONECT   40   39                                                            
MASTER        0    0    0    0    0    0    0    0   40    0   88    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₈H₂₄O₁₂

Average Mass

552.4880 Da

Monoisotopic Mass

552.12678 Da

IUPAC Name

[(2R,3R)-3-(4-hydroxy-3,5-dimethoxyphenyl)-5-methoxy-9-oxo-2H,3H,9H-[1,4]dioxino[2,3-h]chromen-2-yl]methyl 3,4-dihydroxybenzoate

Traditional Name

[(2R,3R)-3-(4-hydroxy-3,5-dimethoxyphenyl)-5-methoxy-9-oxo-2H,3H-[1,4]dioxino[2,3-h]chromen-2-yl]methyl 3,4-dihydroxybenzoate

CAS Registry Number

Not Available

SMILES

COC1=CC(=CC(OC)=C1O)[C@H]1OC2=C(OC)C=C3C=CC(=O)OC3=C2O[C@@H]1COC(=O)C1=CC=C(O)C(O)=C1

InChI Identifier

InChI=1S/C28H24O12/c1-34-18-10-15(11-19(35-2)23(18)32)24-21(12-37-28(33)14-4-6-16(29)17(30)8-14)38-27-25-13(5-7-22(31)39-25)9-20(36-3)26(27)40-24/h4-11,21,24,29-30,32H,12H2,1-3H3/t21-,24-/m1/s1

InChI Key

WQIZCXIRVAHPRD-ZJSXRUAMSA-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
Duranta erecta	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as coumarinolignans. These are lignans with a structure characterized by the presence of a 1,4-dioxane bridge substituted by a phenyl group, and fused to a coumarin.

Kingdom

Organic compounds

Super Class

Lignans, neolignans and related compounds

Class

Coumarinolignans

Sub Class

Not Available

Direct Parent

Coumarinolignans

Alternative Parents

Substituents

Angular-fused coumarolignan skeleton
2-phenylbenzo-1,4-dioxane
Phenylbenzodioxane
P-dioxolo[2,3-h]coumarin
P-hydroxybenzoic acid alkyl ester
M-hydroxybenzoic acid ester
P-hydroxybenzoic acid ester
Dihydroxybenzoic acid
Coumarin
Methoxyphenol
Benzo-1,4-dioxane
Benzodioxane
1-benzopyran
Benzoate ester
Dimethoxybenzene
M-dimethoxybenzene
Benzopyran
Benzoic acid or derivatives
Phenol ether
Catechol
Phenoxy compound
Anisole
Methoxybenzene
Benzoyl
Alkyl aryl ether
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Pyranone
Phenol
Pyran
Benzenoid
Monocyclic benzene moiety
Para-dioxin
Heteroaromatic compound
Carboxylic acid ester
Lactone
Ether
Organoheterocyclic compound
Carboxylic acid derivative
Oxacycle
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	3.56	ChemAxon
pKa (Strongest Acidic)	8.49	ChemAxon
pKa (Strongest Basic)	-4.3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	159.44 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	137.91 m³·mol⁻¹	ChemAxon
Polarizability	54.61 Å³	ChemAxon
Number of Rings	5	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

24710168

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

44583461

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for [(2r,3r)-3-(4-hydroxy-3,5-dimethoxyphenyl)-5-methoxy-9-oxo-2h,3h-[1,4]dioxino[2,3-h]chromen-2-yl]methyl 3,4-dihydroxybenzoate (NP0249046)

MOL for NP0249046 ([(2r,3r)-3-(4-hydroxy-3,5-dimethoxyphenyl)-5-methoxy-9-oxo-2h,3h-[1,4]dioxino[2,3-h]chromen-2-yl]methyl 3,4-dihydroxybenzoate)

3D MOL for NP0249046 ([(2r,3r)-3-(4-hydroxy-3,5-dimethoxyphenyl)-5-methoxy-9-oxo-2h,3h-[1,4]dioxino[2,3-h]chromen-2-yl]methyl 3,4-dihydroxybenzoate)

3D SDF for NP0249046 ([(2r,3r)-3-(4-hydroxy-3,5-dimethoxyphenyl)-5-methoxy-9-oxo-2h,3h-[1,4]dioxino[2,3-h]chromen-2-yl]methyl 3,4-dihydroxybenzoate)

3D-SDF for NP0249046 ([(2r,3r)-3-(4-hydroxy-3,5-dimethoxyphenyl)-5-methoxy-9-oxo-2h,3h-[1,4]dioxino[2,3-h]chromen-2-yl]methyl 3,4-dihydroxybenzoate)

PDB for NP0249046 ([(2r,3r)-3-(4-hydroxy-3,5-dimethoxyphenyl)-5-methoxy-9-oxo-2h,3h-[1,4]dioxino[2,3-h]chromen-2-yl]methyl 3,4-dihydroxybenzoate)

3D PDB for NP0249046 ([(2r,3r)-3-(4-hydroxy-3,5-dimethoxyphenyl)-5-methoxy-9-oxo-2h,3h-[1,4]dioxino[2,3-h]chromen-2-yl]methyl 3,4-dihydroxybenzoate)

SMILES for NP0249046 ([(2r,3r)-3-(4-hydroxy-3,5-dimethoxyphenyl)-5-methoxy-9-oxo-2h,3h-[1,4]dioxino[2,3-h]chromen-2-yl]methyl 3,4-dihydroxybenzoate)

INCHI for NP0249046 ([(2r,3r)-3-(4-hydroxy-3,5-dimethoxyphenyl)-5-methoxy-9-oxo-2h,3h-[1,4]dioxino[2,3-h]chromen-2-yl]methyl 3,4-dihydroxybenzoate)

Structure for NP0249046 ([(2r,3r)-3-(4-hydroxy-3,5-dimethoxyphenyl)-5-methoxy-9-oxo-2h,3h-[1,4]dioxino[2,3-h]chromen-2-yl]methyl 3,4-dihydroxybenzoate)

3D Structure for NP0249046 ([(2r,3r)-3-(4-hydroxy-3,5-dimethoxyphenyl)-5-methoxy-9-oxo-2h,3h-[1,4]dioxino[2,3-h]chromen-2-yl]methyl 3,4-dihydroxybenzoate)