NP-MRD: Showing NP-Card for 4,5-dihydroxy-6-(hydroxymethyl)-2-(1,3,6,7-tetrahydroxy-9-oxoxanthen-2-yl)oxan-3-yl 4-hydroxybenzoate (NP0304993)

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Record Information

Version

2.0

Created at

2022-09-10 20:27:59 UTC

Updated at

2022-09-10 20:27:59 UTC

NP-MRD ID

NP0304993

Secondary Accession Numbers

None

Natural Product Identification

Common Name

4,5-dihydroxy-6-(hydroxymethyl)-2-(1,3,6,7-tetrahydroxy-9-oxoxanthen-2-yl)oxan-3-yl 4-hydroxybenzoate

Description

4,5-Dihydroxy-6-(hydroxymethyl)-2-(1,3,6,7-tetrahydroxy-9-oxo-9H-xanthen-2-yl)oxan-3-yl 4-hydroxybenzoate belongs to the class of organic compounds known as xanthones. These are polycyclic aromatic compounds containing a xanthene moiety conjugated to a ketone group at carbon 9. Xanthene is a tricyclic compound made up of two benzene rings linearly fused to each other through a pyran ring. 4,5-dihydroxy-6-(hydroxymethyl)-2-(1,3,6,7-tetrahydroxy-9-oxoxanthen-2-yl)oxan-3-yl 4-hydroxybenzoate is found in Fridericia samydoides. 4,5-Dihydroxy-6-(hydroxymethyl)-2-(1,3,6,7-tetrahydroxy-9-oxo-9H-xanthen-2-yl)oxan-3-yl 4-hydroxybenzoate is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1533004231515462D          

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M  END

     RDKit          3D

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M  END


  Mrv1533004231515462D          

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 31 32  1  0  0  0  0
 31 33  1  0  0  0  0
 33 34  2  0  0  0  0
 27 34  1  0  0  0  0
 34 35  1  0  0  0  0
 35 36  2  0  0  0  0
 35 37  1  0  0  0  0
 25 37  1  0  0  0  0
 37 38  2  0  0  0  0
 21 38  1  0  0  0  0
 38 39  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0304993

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OCC1OC(C(OC(=O)C2=CC=C(O)C=C2)C(O)C1O)C1=C(O)C=C2OC3=CC(O)=C(O)C=C3C(=O)C2=C1O

> <INCHI_IDENTIFIER>
InChI=1S/C26H22O13/c27-8-17-21(33)23(35)25(39-26(36)9-1-3-10(28)4-2-9)24(38-17)18-14(31)7-16-19(22(18)34)20(32)11-5-12(29)13(30)6-15(11)37-16/h1-7,17,21,23-25,27-31,33-35H,8H2

> <INCHI_KEY>
WVLYNCZFGCFUAG-UHFFFAOYSA-N

> <FORMULA>
C26H22O13

> <MOLECULAR_WEIGHT>
542.449

> <EXACT_MASS>
542.106040768

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_ATOM_COUNT>
61

> <JCHEM_AVERAGE_POLARIZABILITY>
51.96044167375445

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
4,5-dihydroxy-6-(hydroxymethyl)-2-(1,3,6,7-tetrahydroxy-9-oxo-9H-xanthen-2-yl)oxan-3-yl 4-hydroxybenzoate

> <ALOGPS_LOGP>
1.66

> <JCHEM_LOGP>
1.8297925556666665

> <ALOGPS_LOGS>
-2.73

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
7.619067544117975

> <JCHEM_PKA_STRONGEST_ACIDIC>
6.964071608693396

> <JCHEM_PKA_STRONGEST_BASIC>
-2.979193257148019

> <JCHEM_POLAR_SURFACE_AREA>
223.66999999999996

> <JCHEM_REFRACTIVITY>
129.66109999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.02e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
4,5-dihydroxy-6-(hydroxymethyl)-2-(1,3,6,7-tetrahydroxy-9-oxoxanthen-2-yl)oxan-3-yl 4-hydroxybenzoate

> <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  O   UNK     0      -4.001  -5.390   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      -2.667  -4.620   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.334  -5.390   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       0.000  -4.620   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       1.334  -5.390   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.334  -6.930   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       2.667  -7.700   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       2.667  -9.240   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       1.334 -10.010   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       4.001 -10.010   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       5.335  -9.240   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       6.668 -10.010   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       6.668 -11.550   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       8.002 -12.320   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       5.335 -12.320   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       4.001 -11.550   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       0.000  -7.700   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       0.000  -9.240   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0      -1.334  -6.930   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      -2.667  -7.700   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       6.668  -2.310   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0       8.002  -3.080   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       9.336  -2.310   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      10.669  -3.080   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0      12.003  -2.310   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0      10.669  -4.620   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0      12.003  -5.390   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0       9.336  -5.390   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       8.002  -4.620   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       6.668  -5.390   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0       6.668  -6.930   0.000  0.00  0.00           O+0
HETATM   37  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0       4.001  -5.390   0.000  0.00  0.00           C+0
HETATM   39  O   UNK     0       4.001  -6.930   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   19                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   21                                                  
CONECT    6    5    7   17                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11   16                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16                                                       
CONECT   16   15   10                                                       
CONECT   17    6   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17    3   20                                                  
CONECT   20   19                                                            
CONECT   21    5   22   38                                                  
CONECT   22   21   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22   25                                                       
CONECT   25   24   26   37                                                  
CONECT   26   25   27                                                       
CONECT   27   26   28   34                                                  
CONECT   28   27   29                                                       
CONECT   29   28   30   31                                                  
CONECT   30   29                                                            
CONECT   31   29   32   33                                                  
CONECT   32   31                                                            
CONECT   33   31   34                                                       
CONECT   34   33   27   35                                                  
CONECT   35   34   36   37                                                  
CONECT   36   35                                                            
CONECT   37   35   25   38                                                  
CONECT   38   37   21   39                                                  
CONECT   39   38                                                            
MASTER        0    0    0    0    0    0    0    0   39    0   86    0
END

View in JSmol

Synonyms

Value	Source
4,5-Dihydroxy-6-(hydroxymethyl)-2-(1,3,6,7-tetrahydroxy-9-oxo-9H-xanthen-2-yl)oxan-3-yl 4-hydroxybenzoic acid	Generator

Chemical Formula

C₂₆H₂₂O₁₃

Average Mass

542.4490 Da

Monoisotopic Mass

542.10604 Da

IUPAC Name

4,5-dihydroxy-6-(hydroxymethyl)-2-(1,3,6,7-tetrahydroxy-9-oxo-9H-xanthen-2-yl)oxan-3-yl 4-hydroxybenzoate

Traditional Name

4,5-dihydroxy-6-(hydroxymethyl)-2-(1,3,6,7-tetrahydroxy-9-oxoxanthen-2-yl)oxan-3-yl 4-hydroxybenzoate

CAS Registry Number

Not Available

SMILES

OCC1OC(C(OC(=O)C2=CC=C(O)C=C2)C(O)C1O)C1=C(O)C=C2OC3=CC(O)=C(O)C=C3C(=O)C2=C1O

InChI Identifier

InChI=1S/C26H22O13/c27-8-17-21(33)23(35)25(39-26(36)9-1-3-10(28)4-2-9)24(38-17)18-14(31)7-16-19(22(18)34)20(32)11-5-12(29)13(30)6-15(11)37-16/h1-7,17,21,23-25,27-31,33-35H,8H2

InChI Key

WVLYNCZFGCFUAG-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
Fridericia samydoides	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as xanthones. These are polycyclic aromatic compounds containing a xanthene moiety conjugated to a ketone group at carbon 9. Xanthene is a tricyclic compound made up of two benzene rings linearly fused to each other through a pyran ring.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Benzopyrans

Sub Class

1-benzopyrans

Direct Parent

Xanthones

Alternative Parents

Substituents

Phenolic glycoside
Xanthone
P-hydroxybenzoic acid alkyl ester
P-hydroxybenzoic acid ester
Glycosyl compound
Chromone
C-glycosyl compound
Benzoate ester
Benzoic acid or derivatives
Benzoyl
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Phenol
Pyranone
Monocyclic benzene moiety
Monosaccharide
Oxane
Benzenoid
Pyran
Heteroaromatic compound
Vinylogous acid
Carboxylic acid ester
Secondary alcohol
Oxacycle
Carboxylic acid derivative
Polyol
Dialkyl ether
Ether
Primary alcohol
Alcohol
Organic oxygen compound
Organooxygen compound
Organic oxide
Hydrocarbon derivative
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	1.66	ALOGPS
logP	1.83	ChemAxon
logS	-2.7	ALOGPS
pKa (Strongest Acidic)	6.96	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	11	ChemAxon
Hydrogen Donor Count	8	ChemAxon
Polar Surface Area	223.67 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	129.66 m³·mol⁻¹	ChemAxon
Polarizability	51.96 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	No	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

75072233

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 4,5-dihydroxy-6-(hydroxymethyl)-2-(1,3,6,7-tetrahydroxy-9-oxoxanthen-2-yl)oxan-3-yl 4-hydroxybenzoate (NP0304993)

MOL for NP0304993 (4,5-dihydroxy-6-(hydroxymethyl)-2-(1,3,6,7-tetrahydroxy-9-oxoxanthen-2-yl)oxan-3-yl 4-hydroxybenzoate)

3D MOL for NP0304993 (4,5-dihydroxy-6-(hydroxymethyl)-2-(1,3,6,7-tetrahydroxy-9-oxoxanthen-2-yl)oxan-3-yl 4-hydroxybenzoate)

3D SDF for NP0304993 (4,5-dihydroxy-6-(hydroxymethyl)-2-(1,3,6,7-tetrahydroxy-9-oxoxanthen-2-yl)oxan-3-yl 4-hydroxybenzoate)

3D-SDF for NP0304993 (4,5-dihydroxy-6-(hydroxymethyl)-2-(1,3,6,7-tetrahydroxy-9-oxoxanthen-2-yl)oxan-3-yl 4-hydroxybenzoate)

PDB for NP0304993 (4,5-dihydroxy-6-(hydroxymethyl)-2-(1,3,6,7-tetrahydroxy-9-oxoxanthen-2-yl)oxan-3-yl 4-hydroxybenzoate)

3D PDB for NP0304993 (4,5-dihydroxy-6-(hydroxymethyl)-2-(1,3,6,7-tetrahydroxy-9-oxoxanthen-2-yl)oxan-3-yl 4-hydroxybenzoate)

SMILES for NP0304993 (4,5-dihydroxy-6-(hydroxymethyl)-2-(1,3,6,7-tetrahydroxy-9-oxoxanthen-2-yl)oxan-3-yl 4-hydroxybenzoate)

INCHI for NP0304993 (4,5-dihydroxy-6-(hydroxymethyl)-2-(1,3,6,7-tetrahydroxy-9-oxoxanthen-2-yl)oxan-3-yl 4-hydroxybenzoate)

Structure for NP0304993 (4,5-dihydroxy-6-(hydroxymethyl)-2-(1,3,6,7-tetrahydroxy-9-oxoxanthen-2-yl)oxan-3-yl 4-hydroxybenzoate)

3D Structure for NP0304993 (4,5-dihydroxy-6-(hydroxymethyl)-2-(1,3,6,7-tetrahydroxy-9-oxoxanthen-2-yl)oxan-3-yl 4-hydroxybenzoate)