NP-MRD: Showing NP-Card for 2-hydroxy-3,4-dimethoxyxanthen-9-one (NP0324280)

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Record Information

Version

2.0

Created at

2022-09-12 04:15:33 UTC

Updated at

2022-09-12 04:15:33 UTC

NP-MRD ID

NP0324280

Secondary Accession Numbers

None

Natural Product Identification

Common Name

2-hydroxy-3,4-dimethoxyxanthen-9-one

Description

2-Hydroxy-3,4-dimethoxy-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. 2-hydroxy-3,4-dimethoxyxanthen-9-one is found in Hypericum sampsonii. 2-Hydroxy-3,4-dimethoxy-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

 32 34  0  0  0  0  0  0  0  0999 V2000
   -4.4675   -0.3985    0.7123 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6679    0.2375   -0.2887 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3555   -0.1427   -0.4497 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0267   -1.1564   -1.3205 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0424   -1.7730   -2.0195 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7314   -1.5657   -1.5104 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2681   -0.9400   -0.8054 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5790   -1.3279   -0.9736 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8899   -2.2390   -1.7542 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5242   -0.6426   -0.2224 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8497   -0.9798   -0.3428 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8338   -0.3283    0.3834 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4695    0.6750    1.2399 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1388    1.0116    1.3589 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1672    0.3613    0.6356 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9037    0.6817    0.7495 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0538    0.0905    0.0816 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3778    0.4968    0.2646 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7031    1.5201    1.1447 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7316    2.8551    0.6432 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1345   -0.1415    1.7196 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5531   -0.2200    0.5358 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3245   -1.5047    0.5533 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8154   -2.5170   -2.6607 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4697   -2.3536   -2.1863 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1026   -1.7714   -1.0234 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8733   -0.5789    0.3015 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2483    1.1952    1.8187 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8614    1.8058    2.0385 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6826    3.3730    0.9159 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7338    2.8438   -0.4851 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8378    3.4337    0.9458 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
  4  6  1  0
  6  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
 14 15  2  0
 15 16  1  0
 16 17  1  0
 17 18  2  0
 18 19  1  0
 19 20  1  0
 18  3  1  0
 17  7  1  0
 15 10  1  0
  1 21  1  0
  1 22  1  0
  1 23  1  0
  5 24  1  0
  6 25  1  0
 11 26  1  0
 12 27  1  0
 13 28  1  0
 14 29  1  0
 20 30  1  0
 20 31  1  0
 20 32  1  0
M  END


  Mrv1533004251507112D          

 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
    0.7145   -1.2375    0.0000 O   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
    2.8579   -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
    5.0013   -2.8875    0.0000 C   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
    2.1434   -3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -4.1250    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
  4  6  1  0  0  0  0
  6  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
 14 15  2  0  0  0  0
 10 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
  7 17  1  0  0  0  0
 17 18  2  0  0  0  0
  3 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0324280

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=C(O)C=C2C(=O)C3=CC=CC=C3OC2=C1OC

> <INCHI_IDENTIFIER>
InChI=1S/C15H12O5/c1-18-14-10(16)7-9-12(17)8-5-3-4-6-11(8)20-13(9)15(14)19-2/h3-7,16H,1-2H3

> <INCHI_KEY>
QRZSRGUYEIXKQV-UHFFFAOYSA-N

> <FORMULA>
C15H12O5

> <MOLECULAR_WEIGHT>
272.256

> <EXACT_MASS>
272.068473486

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
32

> <JCHEM_AVERAGE_POLARIZABILITY>
27.251170226962348

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
2-hydroxy-3,4-dimethoxy-9H-xanthen-9-one

> <ALOGPS_LOGP>
3.12

> <JCHEM_LOGP>
2.340732367333333

> <ALOGPS_LOGS>
-3.34

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.646956288400979

> <JCHEM_PKA_STRONGEST_BASIC>
-3.740154240957865

> <JCHEM_POLAR_SURFACE_AREA>
64.99000000000001

> <JCHEM_REFRACTIVITY>
71.7236

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.24e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-hydroxy-3,4-dimethoxyxanthen-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  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+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  C   UNK     0       9.336  -5.390   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       8.002  -4.620   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       6.668  -5.390   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       4.001  -5.390   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       4.001  -6.930   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       2.667  -7.700   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   18                                                  
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7                                                       
CONECT    7    6    8   17                                                  
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11   15                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   10   16                                                  
CONECT   16   15   17                                                       
CONECT   17   16    7   18                                                  
CONECT   18   17    3   19                                                  
CONECT   19   18   20                                                       
CONECT   20   19                                                            
MASTER        0    0    0    0    0    0    0    0   20    0   44    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₅H₁₂O₅

Average Mass

272.2560 Da

Monoisotopic Mass

272.06847 Da

IUPAC Name

2-hydroxy-3,4-dimethoxy-9H-xanthen-9-one

Traditional Name

2-hydroxy-3,4-dimethoxyxanthen-9-one

CAS Registry Number

Not Available

SMILES

COC1=C(O)C=C2C(=O)C3=CC=CC=C3OC2=C1OC

InChI Identifier

InChI=1S/C15H12O5/c1-18-14-10(16)7-9-12(17)8-5-3-4-6-11(8)20-13(9)15(14)19-2/h3-7,16H,1-2H3

InChI Key

QRZSRGUYEIXKQV-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
Hypericum sampsonii	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

Xanthone
Chromone
Anisole
1-hydroxy-2-unsubstituted benzenoid
Alkyl aryl ether
Pyranone
Benzenoid
Pyran
Heteroaromatic compound
Ether
Oxacycle
Organic oxygen compound
Hydrocarbon derivative
Organooxygen compound
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	3.12	ALOGPS
logP	2.34	ChemAxon
logS	-3.3	ALOGPS
pKa (Strongest Acidic)	9.65	ChemAxon
pKa (Strongest Basic)	-3.7	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	64.99 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	71.72 m³·mol⁻¹	ChemAxon
Polarizability	27.25 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

493302

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 2-hydroxy-3,4-dimethoxyxanthen-9-one (NP0324280)

MOL for NP0324280 (2-hydroxy-3,4-dimethoxyxanthen-9-one)

3D MOL for NP0324280 (2-hydroxy-3,4-dimethoxyxanthen-9-one)

3D SDF for NP0324280 (2-hydroxy-3,4-dimethoxyxanthen-9-one)

3D-SDF for NP0324280 (2-hydroxy-3,4-dimethoxyxanthen-9-one)

PDB for NP0324280 (2-hydroxy-3,4-dimethoxyxanthen-9-one)

3D PDB for NP0324280 (2-hydroxy-3,4-dimethoxyxanthen-9-one)

SMILES for NP0324280 (2-hydroxy-3,4-dimethoxyxanthen-9-one)

INCHI for NP0324280 (2-hydroxy-3,4-dimethoxyxanthen-9-one)

Structure for NP0324280 (2-hydroxy-3,4-dimethoxyxanthen-9-one)

3D Structure for NP0324280 (2-hydroxy-3,4-dimethoxyxanthen-9-one)