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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-11 17:38:38 UTC

Update Date

2022-03-07 02:52:40 UTC

HMDB ID

HMDB0030723

Secondary Accession Numbers

HMDB30723

Metabolite Identification

Common Name

1,5-Dihydroxyxanthone

Description

1,5-Dihydroxyxanthone 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-Dihydroxyxanthone has been detected, but not quantified in, fruits and mammee apples (Mammea americana). This could make 1,5-dihydroxyxanthone a potential biomarker for the consumption of these foods. Based on a literature review a significant number of articles have been published on 1,5-Dihydroxyxanthone.

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

  Mrv0541 05061305282D          

 17 19  0  0  0  0            999 V2000
   -1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.8250    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
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    2.0625    0.0000 O   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
    0.7145    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  2  0  0  0  0
  4  2  2  0  0  0  0
  5  1  1  0  0  0  0
  6  2  1  0  0  0  0
  7  3  1  0  0  0  0
  8  4  1  0  0  0  0
  9  5  2  0  0  0  0
 10  6  2  0  0  0  0
 11  8  2  0  0  0  0
 11 10  1  0  0  0  0
 12  7  1  0  0  0  0
 12 11  1  0  0  0  0
 13  7  2  0  0  0  0
 13  9  1  0  0  0  0
 14  8  1  0  0  0  0
 15  9  1  0  0  0  0
 16 12  2  0  0  0  0
 17 10  1  0  0  0  0
 17 13  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0030723

> <DATABASE_NAME>
hmdb

> <SMILES>
OC1=CC=CC2=C1OC1=CC=CC(O)=C1C2=O

> <INCHI_IDENTIFIER>
InChI=1S/C13H8O4/c14-8-4-2-6-10-11(8)12(16)7-3-1-5-9(15)13(7)17-10/h1-6,14-15H

> <INCHI_KEY>
APIPFXZYOMIJQG-UHFFFAOYSA-N

> <FORMULA>
C13H8O4

> <MOLECULAR_WEIGHT>
228.2002

> <EXACT_MASS>
228.042258744

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
22.104149838637642

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
1,5-dihydroxy-9H-xanthen-9-one

> <ALOGPS_LOGP>
2.79

> <JCHEM_LOGP>
3.0025095769999997

> <ALOGPS_LOGS>
-2.68

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
9.6315495868024

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.877761265199458

> <JCHEM_PKA_STRONGEST_BASIC>
-4.466798260801302

> <JCHEM_POLAR_SURFACE_AREA>
66.76

> <JCHEM_REFRACTIVITY>
60.778100000000016

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.76e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1,5-dihydroxyxanthen-9-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 06-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAY-13         0                                  
HETATM    1  C   UNK     0      -2.667   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -2.667   1.540   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -1.334   2.310   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       4.001  -2.310   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0      -1.334   3.850   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       1.334   2.310   0.000  0.00  0.00           O+0
CONECT    1    3    5                                                       
CONECT    2    4    6                                                       
CONECT    3    1    7                                                       
CONECT    4    2    8                                                       
CONECT    5    1    9                                                       
CONECT    6    2   10                                                       
CONECT    7    3   12   13                                                  
CONECT    8    4   11   14                                                  
CONECT    9    5   13   15                                                  
CONECT   10    6   11   17                                                  
CONECT   11    8   10   12                                                  
CONECT   12    7   11   16                                                  
CONECT   13    7    9   17                                                  
CONECT   14    8                                                            
CONECT   15    9                                                            
CONECT   16   12                                                            
CONECT   17   10   13                                                       
MASTER        0    0    0    0    0    0    0    0   17    0   38    0
END

View in JSmol View Stereo Labels

Synonyms

Value	Source
1,5-Dihydroxy-9H-xanthen-9-one, 9ci	HMDB
6-(3,3-Dimethylallyl)-1,5-dihydroxyxanthone	HMDB
Calophyllin b	HMDB

Chemical Formula

C₁₃H₈O₄

Average Molecular Weight

228.2002

Monoisotopic Molecular Weight

228.042258744

IUPAC Name

1,5-dihydroxy-9H-xanthen-9-one

Traditional Name

1,5-dihydroxyxanthen-9-one

CAS Registry Number

14686-65-8

SMILES

OC1=CC=CC2=C1OC1=CC=CC(O)=C1C2=O

InChI Identifier

InChI=1S/C13H8O4/c14-8-4-2-6-10-11(8)12(16)7-3-1-5-9(15)13(7)17-10/h1-6,14-15H

InChI Key

APIPFXZYOMIJQG-UHFFFAOYSA-N

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
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Pyranone
Benzenoid
Pyran
Heteroaromatic compound
Vinylogous acid
Oxacycle
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Membrane (HMDB: HMDB0030723)
Cell membrane (HMDB: HMDB0030723)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0030723)

Source

Endogenous

Endogenous (HMDB: HMDB0030723)

Plant

Plant (HMDB: HMDB0030723)

Exogenous

Food

Food (HMDB: HMDB0030723)

Fruit

Tropical fruit

Mammee apple (FooDB: FOOD00405)

Fruits (FooDB: FOOD00871)

Exogenous (HMDB: HMDB0030723)

Process

Not Available

Role

Not Available

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	286 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	0.48 g/L	ALOGPS
logP	2.79	ALOGPS
logP	3	ChemAxon
logS	-2.7	ALOGPS
pKa (Strongest Acidic)	7.88	ChemAxon
pKa (Strongest Basic)	-4.5	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	66.76 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	60.78 m³·mol⁻¹	ChemAxon
Polarizability	22.1 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

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	149.642	31661259
DarkChem	[M-H]-	148.75	31661259
DeepCCS	[M+H]+	144.659	30932474
DeepCCS	[M-H]-	142.301	30932474
DeepCCS	[M-2H]-	176.139	30932474
DeepCCS	[M+Na]+	150.956	30932474
AllCCS	[M+H]+	148.4	32859911
AllCCS	[M+H-H2O]+	144.1	32859911
AllCCS	[M+NH4]+	152.4	32859911
AllCCS	[M+Na]+	153.5	32859911
AllCCS	[M-H]-	148.2	32859911
AllCCS	[M+Na-2H]-	147.5	32859911
AllCCS	[M+HCOO]-	146.8	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
1,5-Dihydroxyxanthone	OC1=CC=CC2=C1OC1=CC=CC(O)=C1C2=O	3397.0	Standard polar	33892256
1,5-Dihydroxyxanthone	OC1=CC=CC2=C1OC1=CC=CC(O)=C1C2=O	2264.2	Standard non polar	33892256
1,5-Dihydroxyxanthone	OC1=CC=CC2=C1OC1=CC=CC(O)=C1C2=O	2164.8	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
1,5-Dihydroxyxanthone,1TMS,isomer #1	C[Si](C)(C)OC1=CC=CC2=C1OC1=CC=CC(O)=C1C2=O	2561.8	Semi standard non polar	33892256
1,5-Dihydroxyxanthone,1TMS,isomer #2	C[Si](C)(C)OC1=CC=CC2=C1C(=O)C1=CC=CC(O)=C1O2	2572.8	Semi standard non polar	33892256
1,5-Dihydroxyxanthone,2TMS,isomer #1	C[Si](C)(C)OC1=CC=CC2=C1OC1=CC=CC(O[Si](C)(C)C)=C1C2=O	2647.0	Semi standard non polar	33892256
1,5-Dihydroxyxanthone,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC1=CC=CC2=C1OC1=CC=CC(O)=C1C2=O	2790.2	Semi standard non polar	33892256
1,5-Dihydroxyxanthone,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC1=CC=CC2=C1C(=O)C1=CC=CC(O)=C1O2	2798.3	Semi standard non polar	33892256
1,5-Dihydroxyxanthone,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC1=CC=CC2=C1OC1=CC=CC(O[Si](C)(C)C(C)(C)C)=C1C2=O	3081.0	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - 1,5-Dihydroxyxanthone GC-MS (Non-derivatized) - 70eV, Positive	splash10-0fba-1790000000-3e72e24024d2a88f1c16	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 1,5-Dihydroxyxanthone GC-MS (2 TMS) - 70eV, Positive	splash10-05fr-5595000000-7c1bb6ad674eaf5ce233	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 1,5-Dihydroxyxanthone GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 1,5-Dihydroxyxanthone GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1,5-Dihydroxyxanthone 10V, Positive-QTOF	splash10-004i-0090000000-71bfe2c1bd7958dbf3ce	2016-08-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1,5-Dihydroxyxanthone 20V, Positive-QTOF	splash10-004i-0090000000-e88330be24a280c5ab26	2016-08-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1,5-Dihydroxyxanthone 40V, Positive-QTOF	splash10-0kdi-6960000000-cb601c829d0f04278472	2016-08-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1,5-Dihydroxyxanthone 10V, Negative-QTOF	splash10-004i-0090000000-09e99672fa9d99f0ad2b	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1,5-Dihydroxyxanthone 20V, Negative-QTOF	splash10-004i-0090000000-974204cce3ba876be748	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1,5-Dihydroxyxanthone 40V, Negative-QTOF	splash10-00p0-4970000000-68c124f3fcf1c368069b	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1,5-Dihydroxyxanthone 10V, Negative-QTOF	splash10-004i-0090000000-d8e725b6742766a16bb5	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1,5-Dihydroxyxanthone 20V, Negative-QTOF	splash10-004i-0090000000-d8e725b6742766a16bb5	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1,5-Dihydroxyxanthone 40V, Negative-QTOF	splash10-00kk-3900000000-a08c38ac4b419eb3894c	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1,5-Dihydroxyxanthone 10V, Positive-QTOF	splash10-004i-0090000000-02cbe499adea44a39627	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1,5-Dihydroxyxanthone 20V, Positive-QTOF	splash10-004i-0090000000-02cbe499adea44a39627	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1,5-Dihydroxyxanthone 40V, Positive-QTOF	splash10-0fi0-2910000000-68fd6f959f7b3d4a4f67	2021-09-24	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Membrane

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5480299

PDB ID

Not Available

ChEBI ID

411468

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

(). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .

Showing metabocard for 1,5-Dihydroxyxanthone (HMDB0030723)

MOL for HMDB0030723 (1,5-Dihydroxyxanthone)

3D MOL for HMDB0030723 (1,5-Dihydroxyxanthone)

3D SDF for HMDB0030723 (1,5-Dihydroxyxanthone)

3D-SDF for HMDB0030723 (1,5-Dihydroxyxanthone)

PDB for HMDB0030723 (1,5-Dihydroxyxanthone)

3D PDB for HMDB0030723 (1,5-Dihydroxyxanthone)

SMILES for HMDB0030723 (1,5-Dihydroxyxanthone)

INCHI for HMDB0030723 (1,5-Dihydroxyxanthone)

Structure for HMDB0030723 (1,5-Dihydroxyxanthone)

3D Structure for HMDB0030723 (1,5-Dihydroxyxanthone)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra