NP-MRD: Showing NP-Card for 1,5,6-Trihydroxy-3-methoxyxanthone (NP0138319)

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Record Information

Version

1.0

Created at

2022-05-31 17:55:04 UTC

Updated at

2022-05-31 17:55:04 UTC

NP-MRD ID

NP0138319

Secondary Accession Numbers

None

Natural Product Identification

Common Name

1,5,6-Trihydroxy-3-methoxyxanthone

Description

1,5,6-Trihydroxy-3-methoxy-9H-xanthen-9-one 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. 1,5,6-Trihydroxy-3-methoxy-9H-xanthen-9-one is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 30 32  0  0  0  0  0  0  0  0999 V2000
    5.3418   -0.0389    0.3981 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2294    0.8321    0.4528 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9500    0.2587    0.3124 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7911   -1.0849    0.1307 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5299   -1.6940   -0.0134 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4490   -3.0265   -0.1896 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4389   -0.8797    0.0352 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8591   -1.3772   -0.0964 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0849   -2.5817   -0.2636 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9695   -0.5386   -0.0457 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2611   -1.0079   -0.1733 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3519   -0.1405   -0.1179 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1453    1.2052    0.0666 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2451    2.0617    0.1202 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8473    1.6454    0.1908 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6515    3.0224    0.3788 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7455    0.8091    0.1400 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5193    1.2543    0.2611 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5560    0.4980    0.2192 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8167    1.0288    0.3531 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3846   -0.4592   -0.6329 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2746    0.5027    0.6565 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2359   -0.8850    1.1218 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6789   -1.7118    0.0958 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7447   -3.6649   -0.3086 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4037   -2.0620   -0.3168 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3664   -0.5215   -0.2197 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1452    3.0598    0.2543 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7374    3.3981    0.4747 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9114    2.0980    0.4961 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  5  7  2  0
  7  8  1  0
  8  9  2  0
  8 10  1  0
 10 11  2  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
 13 15  1  0
 15 16  1  0
 15 17  2  0
 17 18  1  0
 18 19  1  0
 19 20  2  0
 20  3  1  0
 19  7  1  0
 17 10  1  0
  1 21  1  0
  1 22  1  0
  1 23  1  0
  4 24  1  0
  6 25  1  0
 11 26  1  0
 12 27  1  0
 14 28  1  0
 16 29  1  0
 20 30  1  0
M  END


  Mrv1533004251523522D          

 20 22  0  0  0  0            999 V2000
    0.7145   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -2.8875    0.0000 O   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
    1.4289   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
 10 11  2  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
 13 15  1  0  0  0  0
 15 16  1  0  0  0  0
 15 17  2  0  0  0  0
 10 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
  7 19  1  0  0  0  0
 19 20  2  0  0  0  0
  3 20  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0138319

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=CC(O)=C2C(=O)C3=CC=C(O)C(O)=C3OC2=C1

> <INCHI_IDENTIFIER>
InChI=1S/C14H10O6/c1-19-6-4-9(16)11-10(5-6)20-14-7(12(11)17)2-3-8(15)13(14)18/h2-5,15-16,18H,1H3

> <INCHI_KEY>
JHOYIGDPCIBYKV-UHFFFAOYSA-N

> <FORMULA>
C14H10O6

> <MOLECULAR_WEIGHT>
274.228

> <EXACT_MASS>
274.047738042

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
30

> <JCHEM_AVERAGE_POLARIZABILITY>
26.28733008343376

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
1,5,6-trihydroxy-3-methoxy-9H-xanthen-9-one

> <ALOGPS_LOGP>
2.55

> <JCHEM_LOGP>
2.5412729896666666

> <ALOGPS_LOGS>
-2.85

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
8.434133497063169

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.484411253525969

> <JCHEM_PKA_STRONGEST_BASIC>
-3.7790501406133017

> <JCHEM_POLAR_SURFACE_AREA>
96.22000000000001

> <JCHEM_REFRACTIVITY>
69.22220000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.88e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1,5,6-trihydroxy-3-methoxyxanthen-9-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 25-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   25-APR-15         0                                  
HETATM    1  C   UNK     0       1.334  -6.930   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       1.334  -5.390   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       4.001  -0.770   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       6.668  -2.310   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       6.668  -0.770   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       8.002  -3.080   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       9.336  -2.310   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      10.669  -3.080   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      10.669  -4.620   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      12.003  -5.390   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       9.336  -5.390   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       9.336  -6.930   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       8.002  -4.620   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       6.668  -5.390   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       4.001  -5.390   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   20                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8   19                                                  
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11   17                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15   10   18                                                  
CONECT   18   17   19                                                       
CONECT   19   18    7   20                                                  
CONECT   20   19    3                                                       
MASTER        0    0    0    0    0    0    0    0   20    0   44    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₄H₁₀O₆

Average Mass

274.2280 Da

Monoisotopic Mass

274.04774 Da

IUPAC Name

1,5,6-trihydroxy-3-methoxy-9H-xanthen-9-one

Traditional Name

1,5,6-trihydroxy-3-methoxyxanthen-9-one

CAS Registry Number

50868-52-5

SMILES

COC1=CC(O)=C2C(=O)C3=CC=C(O)C(O)=C3OC2=C1

InChI Identifier

InChI=1S/C14H10O6/c1-19-6-4-9(16)11-10(5-6)20-14-7(12(11)17)2-3-8(15)13(14)18/h2-5,15-16,18H,1H3

InChI Key

JHOYIGDPCIBYKV-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, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Not Available

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

Xanthone
Chromone
Anisole
Phenol ether
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Alkyl aryl ether
Phenol
Pyranone
Benzenoid
Pyran
Heteroaromatic compound
Vinylogous acid
Oxacycle
Ether
Polyol
Organic oxygen compound
Organooxygen compound
Hydrocarbon derivative
Organic oxide
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	2.55	ALOGPS
logP	2.54	ChemAxon
logS	-2.8	ALOGPS
pKa (Strongest Acidic)	7.48	ChemAxon
pKa (Strongest Basic)	-3.8	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	96.22 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	69.22 m³·mol⁻¹	ChemAxon
Polarizability	26.29 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	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

86219227

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for 1,5,6-Trihydroxy-3-methoxyxanthone (NP0138319)

MOL for NP0138319 (1,5,6-Trihydroxy-3-methoxyxanthone)

3D MOL for NP0138319 (1,5,6-Trihydroxy-3-methoxyxanthone)

3D SDF for NP0138319 (1,5,6-Trihydroxy-3-methoxyxanthone)

3D-SDF for NP0138319 (1,5,6-Trihydroxy-3-methoxyxanthone)

PDB for NP0138319 (1,5,6-Trihydroxy-3-methoxyxanthone)

3D PDB for NP0138319 (1,5,6-Trihydroxy-3-methoxyxanthone)

SMILES for NP0138319 (1,5,6-Trihydroxy-3-methoxyxanthone)

INCHI for NP0138319 (1,5,6-Trihydroxy-3-methoxyxanthone)

Structure for NP0138319 (1,5,6-Trihydroxy-3-methoxyxanthone)

3D Structure for NP0138319 (1,5,6-Trihydroxy-3-methoxyxanthone)