NP-MRD: Showing NP-Card for 2-(hydroxymethyl)-3-(3-methoxy-4-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)-2h,3h-[1,4]dioxino[2,3-h]chromen-9-one (NP0141516)

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Record Information

Version

2.0

Created at

2022-09-01 19:51:32 UTC

Updated at

2022-09-01 19:51:32 UTC

NP-MRD ID

NP0141516

Secondary Accession Numbers

None

Natural Product Identification

Common Name

2-(hydroxymethyl)-3-(3-methoxy-4-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)-2h,3h-[1,4]dioxino[2,3-h]chromen-9-one

Description

2-(Hydroxymethyl)-3-(3-methoxy-4-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)-2H,3H,9H-[1,4]dioxino[2,3-h]chromen-9-one 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. 2-(hydroxymethyl)-3-(3-methoxy-4-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)-2h,3h-[1,4]dioxino[2,3-h]chromen-9-one is found in Daphne feddei. 2-(Hydroxymethyl)-3-(3-methoxy-4-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)-2H,3H,9H-[1,4]dioxino[2,3-h]chromen-9-one is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1533004231522472D          

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M  END

     RDKit          3D

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M  END


  Mrv1533004231522472D          

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 31 32  1  0  0  0  0
 26 32  1  0  0  0  0
 32 33  2  0  0  0  0
 23 33  1  0  0  0  0
 33 34  1  0  0  0  0
 34 35  1  0  0  0  0
 21 35  1  0  0  0  0
 35 36  1  0  0  0  0
 36 37  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0141516

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=CC(=CC=C1OC1OC(CO)C(O)C(O)C1O)C1OC2=CC=C3C=CC(=O)OC3=C2OC1CO

> <INCHI_IDENTIFIER>
InChI=1S/C25H26O12/c1-32-15-8-12(3-5-13(15)35-25-21(31)20(30)19(29)16(9-26)36-25)22-17(10-27)34-24-14(33-22)6-2-11-4-7-18(28)37-23(11)24/h2-8,16-17,19-22,25-27,29-31H,9-10H2,1H3

> <INCHI_KEY>
YMHNZLAKKRLTCY-UHFFFAOYSA-N

> <FORMULA>
C25H26O12

> <MOLECULAR_WEIGHT>
518.471

> <EXACT_MASS>
518.142426277

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_ATOM_COUNT>
63

> <JCHEM_AVERAGE_POLARIZABILITY>
50.893074448551786

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-(hydroxymethyl)-3-(3-methoxy-4-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)-2H,3H,9H-[1,4]dioxino[2,3-h]chromen-9-one

> <ALOGPS_LOGP>
0.64

> <JCHEM_LOGP>
-0.27890729466666664

> <ALOGPS_LOGS>
-2.90

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.179609212692789

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.198130756113994

> <JCHEM_PKA_STRONGEST_BASIC>
-2.981092354907191

> <JCHEM_POLAR_SURFACE_AREA>
173.6

> <JCHEM_REFRACTIVITY>
123.33979999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
6.46e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-(hydroxymethyl)-3-(3-methoxy-4-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)-2H,3H-[1,4]dioxino[2,3-h]chromen-9-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 23-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-APR-15         0                                  
HETATM    1  C   UNK     0      -2.365   1.127   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       1.485  -2.874   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -0.055  -2.874   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -0.825  -1.540   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -2.365  -1.540   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      -3.135  -2.874   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -2.365  -4.207   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      -3.135  -5.541   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -2.365  -6.875   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      -3.135  -8.208   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0      -4.675  -5.541   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      -5.445  -6.875   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0      -5.445  -4.207   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      -6.985  -4.207   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0      -4.675  -2.874   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      -5.445  -1.540   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       3.795  -1.540   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       4.565  -0.206   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0       6.105  -0.206   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       6.875   1.127   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       8.415   1.127   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       9.185  -0.206   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      10.725  -0.206   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      11.495  -1.540   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      10.725  -2.874   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0      11.495  -4.207   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0       9.185  -2.874   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0       8.415  -1.540   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       6.875  -1.540   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0       6.105  -2.874   0.000  0.00  0.00           O+0
HETATM   35  C   UNK     0       4.565  -2.874   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0       3.795  -4.207   0.000  0.00  0.00           C+0
HETATM   37  O   UNK     0       2.255  -4.207   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    8                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   21                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    3    9                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11   19                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13   15                                                  
CONECT   13   12   14                                                       
CONECT   14   13                                                            
CONECT   15   12   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   10   20                                                  
CONECT   20   19                                                            
CONECT   21    5   22   35                                                  
CONECT   22   21   23                                                       
CONECT   23   22   24   33                                                  
CONECT   24   23   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27   32                                                  
CONECT   27   26   28                                                       
CONECT   28   27   29                                                       
CONECT   29   28   30   31                                                  
CONECT   30   29                                                            
CONECT   31   29   32                                                       
CONECT   32   31   26   33                                                  
CONECT   33   32   23   34                                                  
CONECT   34   33   35                                                       
CONECT   35   34   21   36                                                  
CONECT   36   35   37                                                       
CONECT   37   36                                                            
MASTER        0    0    0    0    0    0    0    0   37    0   82    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₅H₂₆O₁₂

Average Mass

518.4710 Da

Monoisotopic Mass

518.14243 Da

IUPAC Name

2-(hydroxymethyl)-3-(3-methoxy-4-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)-2H,3H,9H-[1,4]dioxino[2,3-h]chromen-9-one

Traditional Name

2-(hydroxymethyl)-3-(3-methoxy-4-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)-2H,3H-[1,4]dioxino[2,3-h]chromen-9-one

CAS Registry Number

Not Available

SMILES

COC1=CC(=CC=C1OC1OC(CO)C(O)C(O)C1O)C1OC2=CC=C3C=CC(=O)OC3=C2OC1CO

InChI Identifier

InChI=1S/C25H26O12/c1-32-15-8-12(3-5-13(15)35-25-21(31)20(30)19(29)16(9-26)36-25)22-17(10-27)34-24-14(33-22)6-2-11-4-7-18(28)37-23(11)24/h2-8,16-17,19-22,25-27,29-31H,9-10H2,1H3

InChI Key

YMHNZLAKKRLTCY-UHFFFAOYSA-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
Daphne feddei	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
Phenolic glycoside
P-dioxolo[2,3-h]coumarin
Hexose monosaccharide
Coumarin
Glycosyl compound
O-glycosyl compound
Benzo-1,4-dioxane
Benzodioxane
Benzopyran
1-benzopyran
Anisole
Phenoxy compound
Methoxybenzene
Phenol ether
Pyranone
Alkyl aryl ether
Benzenoid
Pyran
Para-dioxin
Oxane
Monocyclic benzene moiety
Monosaccharide
Heteroaromatic compound
Secondary alcohol
Lactone
Acetal
Polyol
Organoheterocyclic compound
Oxacycle
Ether
Alcohol
Primary alcohol
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
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	0.64	ALOGPS
logP	-0.28	ChemAxon
logS	-2.9	ALOGPS
pKa (Strongest Acidic)	12.2	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	11	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	173.6 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	123.34 m³·mol⁻¹	ChemAxon
Polarizability	50.89 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

75115390

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 2-(hydroxymethyl)-3-(3-methoxy-4-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)-2h,3h-[1,4]dioxino[2,3-h]chromen-9-one (NP0141516)

MOL for NP0141516 (2-(hydroxymethyl)-3-(3-methoxy-4-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)-2h,3h-[1,4]dioxino[2,3-h]chromen-9-one)

3D MOL for NP0141516 (2-(hydroxymethyl)-3-(3-methoxy-4-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)-2h,3h-[1,4]dioxino[2,3-h]chromen-9-one)

3D SDF for NP0141516 (2-(hydroxymethyl)-3-(3-methoxy-4-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)-2h,3h-[1,4]dioxino[2,3-h]chromen-9-one)

3D-SDF for NP0141516 (2-(hydroxymethyl)-3-(3-methoxy-4-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)-2h,3h-[1,4]dioxino[2,3-h]chromen-9-one)

PDB for NP0141516 (2-(hydroxymethyl)-3-(3-methoxy-4-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)-2h,3h-[1,4]dioxino[2,3-h]chromen-9-one)

3D PDB for NP0141516 (2-(hydroxymethyl)-3-(3-methoxy-4-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)-2h,3h-[1,4]dioxino[2,3-h]chromen-9-one)

SMILES for NP0141516 (2-(hydroxymethyl)-3-(3-methoxy-4-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)-2h,3h-[1,4]dioxino[2,3-h]chromen-9-one)

INCHI for NP0141516 (2-(hydroxymethyl)-3-(3-methoxy-4-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)-2h,3h-[1,4]dioxino[2,3-h]chromen-9-one)

Structure for NP0141516 (2-(hydroxymethyl)-3-(3-methoxy-4-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)-2h,3h-[1,4]dioxino[2,3-h]chromen-9-one)

3D Structure for NP0141516 (2-(hydroxymethyl)-3-(3-methoxy-4-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)-2h,3h-[1,4]dioxino[2,3-h]chromen-9-one)