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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-11 17:30:31 UTC

Update Date

2023-02-21 17:18:47 UTC

HMDB ID

HMDB0029457

Secondary Accession Numbers

HMDB29457

Metabolite Identification

Common Name

Xanthotoxol

Description

Xanthotoxol, also known as 8-hydroxypsoralen, belongs to the class of organic compounds known as 8-hydroxypsoralens. These are psoralens containing a hydroxyl group attached at the C8 position of the psoralen group. Xanthotoxol exists in all living organisms, ranging from bacteria to humans. Xanthotoxol has been detected, but not quantified in, several different foods, such as parsnips (Pastinaca sativa), herbs and spices, parsleys (Petroselinum crispum), fats and oils, and root vegetables. This could make xanthotoxol a potential biomarker for the consumption of these foods. Xanthotoxol is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. Based on a literature review a significant number of articles have been published on Xanthotoxol.

Structure

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

Xanthotoxol
  Mrv1572001071617272D          

 21 23  0  0  0  0            999 V2000
    6.0576    0.1379    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1105    0.3275    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5624    1.1239    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500    0.3189    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2769   -0.9386    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8480   -0.9386    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2769   -0.1136    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8480   -0.1136    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5624   -1.3511    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5624    0.2989    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0576   -1.1900    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1105   -1.3797    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5391   -0.5261    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3629   -0.9558    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3629   -0.0964    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5624   -1.8626    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2165   -1.6762    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1163   -1.8912    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.0506   -0.5261    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9210   -1.2133    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0055    1.3797    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  7  1  0  0  0  0
  1 13  1  0  0  0  0
  2  8  1  0  0  0  0
  2 15  1  0  0  0  0
  3 10  1  0  0  0  0
  3 21  1  0  0  0  0
  4 15  2  0  0  0  0
  5  7  2  0  0  0  0
  5  9  1  0  0  0  0
  5 11  1  0  0  0  0
  6  8  1  0  0  0  0
  6  9  2  0  0  0  0
  6 12  1  0  0  0  0
  7 10  1  0  0  0  0
  8 10  2  0  0  0  0
  9 16  1  0  0  0  0
 11 13  2  0  0  0  0
 11 17  1  0  0  0  0
 12 14  2  0  0  0  0
 12 18  1  0  0  0  0
 13 19  1  0  0  0  0
 14 15  1  0  0  0  0
 14 20  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0029457

> <DATABASE_NAME>
hmdb

> <SMILES>
[H]OC1=C2OC(=O)C([H])=C([H])C2=C([H])C2=C1OC([H])=C2[H]

> <INCHI_IDENTIFIER>
InChI=1S/C11H6O4/c12-8-2-1-6-5-7-3-4-14-10(7)9(13)11(6)15-8/h1-5,13H

> <INCHI_KEY>
JWVYQQGERKEAHW-UHFFFAOYSA-N

> <FORMULA>
C11H6O4

> <MOLECULAR_WEIGHT>
202.165

> <EXACT_MASS>
202.026608673

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
21

> <JCHEM_AVERAGE_POLARIZABILITY>
19.008932072653543

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
9-hydroxy-7H-furo[3,2-g]chromen-7-one

> <ALOGPS_LOGP>
1.90

> <JCHEM_LOGP>
2.288917694333333

> <ALOGPS_LOGS>
-2.42

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.19114208397817

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9271450364723006

> <JCHEM_POLAR_SURFACE_AREA>
59.67

> <JCHEM_REFRACTIVITY>
52.3706

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.77e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
xanthotoxol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 07-JAN-16   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: Xanthotoxol                                       
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   07-JAN-16         0                                  
HETATM    1  O   UNK     0      11.308   0.257   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0       5.806   0.611   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0       8.516   2.098   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0       3.080   0.595   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       9.850  -1.752   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       7.183  -1.752   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       9.850  -0.212   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       7.183  -0.212   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       8.516  -2.522   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       8.516   0.558   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      11.308  -2.221   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       5.806  -2.575   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      12.206  -0.982   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.411  -1.784   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       4.411  -0.180   0.000  0.00  0.00           C+0
HETATM   16  H   UNK     0       8.516  -3.477   0.000  0.00  0.00           H+0
HETATM   17  H   UNK     0      11.604  -3.129   0.000  0.00  0.00           H+0
HETATM   18  H   UNK     0       5.817  -3.530   0.000  0.00  0.00           H+0
HETATM   19  H   UNK     0      13.161  -0.982   0.000  0.00  0.00           H+0
HETATM   20  H   UNK     0       3.586  -2.265   0.000  0.00  0.00           H+0
HETATM   21  H   UNK     0       9.344   2.575   0.000  0.00  0.00           H+0
CONECT    1    7   13                                                       
CONECT    2    8   15                                                       
CONECT    3   10   21                                                       
CONECT    4   15                                                            
CONECT    5    7    9   11                                                  
CONECT    6    8    9   12                                                  
CONECT    7    1    5   10                                                  
CONECT    8    2    6   10                                                  
CONECT    9    5    6   16                                                  
CONECT   10    3    7    8                                                  
CONECT   11    5   13   17                                                  
CONECT   12    6   14   18                                                  
CONECT   13    1   11   19                                                  
CONECT   14   12   15   20                                                  
CONECT   15    2    4   14                                                  
CONECT   16    9                                                            
CONECT   17   11                                                            
CONECT   18   12                                                            
CONECT   19   13                                                            
CONECT   20   14                                                            
CONECT   21    3                                                            
MASTER        0    0    0    0    0    0    0    0   21    0   46    0
END

View in JSmol View Stereo Labels

Synonyms

Value	Source
8-Hydroxyfuranocoumarin	ChEBI
8-Hydroxypsoralen	ChEBI

Chemical Formula

C₁₁H₆O₄

Average Molecular Weight

202.165

Monoisotopic Molecular Weight

202.026608673

IUPAC Name

9-hydroxy-7H-furo[3,2-g]chromen-7-one

Traditional Name

xanthotoxol

CAS Registry Number

2009-24-7

SMILES

[H]OC1=C2OC(=O)C([H])=C([H])C2=C([H])C2=C1OC([H])=C2[H]

InChI Identifier

InChI=1S/C11H6O4/c12-8-2-1-6-5-7-3-4-14-10(7)9(13)11(6)15-8/h1-5,13H

InChI Key

JWVYQQGERKEAHW-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 8-hydroxypsoralens. These are psoralens containing a hydroxyl group attached at the C8 position of the psoralen group.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Coumarins and derivatives

Sub Class

Furanocoumarins

Direct Parent

8-hydroxypsoralens

Alternative Parents

Substituents

8-hydroxypsoralen
Benzopyran
1-benzopyran
Benzofuran
1-hydroxy-4-unsubstituted benzenoid
Pyranone
Pyran
Benzenoid
Furan
Heteroaromatic compound
Lactone
Oxacycle
Organoheterocyclic compound
Organooxygen compound
Organic oxygen compound
Hydrocarbon derivative
Organic oxide
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

8-hydroxyfurocoumarin (CHEBI:15709 )
Furanocoumarins (C00841 )
an 8-hydroxyfurocoumarin (CPD-13041 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Extracellular (HMDB: HMDB0029457)
Cytoplasm (HMDB: HMDB0029457)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0029457)

Source

Endogenous

Endogenous (HMDB: HMDB0029457)

Plant

Plant (HMDB: HMDB0029457)

Exogenous

Food

Food (HMDB: HMDB0029457)

Fruit

Other fruit

Fig (FooDB: FOOD00081)

Fruits (FooDB: FOOD00871)

Herb and spice

Herb

Parsley (FooDB: FOOD00131)

Herbs and Spices (FooDB: FOOD00866)

Vegetable

Root vegetable

Parsnip (FooDB: FOOD00129)
Root vegetables (FooDB: FOOD00873)

Leaf vegetable

Green vegetables (FooDB: FOOD00872)

Fat and oil

Fats and oils (FooDB: FOOD00864)

Exogenous (HMDB: HMDB0029457)

Process

Not Available

Role

Biological role

Industrial application

Pharmaceutical industry

Antineoplastic agent

Cancer preventive (HMDB: HMDB0029457)

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	251 - 252 °C	Not Available
Boiling Point	428.00 to 429.00 °C. @ 760.00 mm Hg (est)	The Good Scents Company Information System
Water Solubility	7279 mg/L @ 25 °C (est)	The Good Scents Company Information System
LogP	1.405 (est)	The Good Scents Company Information System

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	0.78 g/L	ALOGPS
logP	1.9	ALOGPS
logP	2.29	ChemAxon
logS	-2.4	ALOGPS
pKa (Strongest Acidic)	8.19	ChemAxon
pKa (Strongest Basic)	-2.9	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	59.67 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	52.37 m³·mol⁻¹	ChemAxon
Polarizability	19.01 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]+	142.766	31661259
DarkChem	[M-H]-	141.902	31661259
DeepCCS	[M+H]+	153.888	30932474
DeepCCS	[M-H]-	151.492	30932474
DeepCCS	[M-2H]-	184.997	30932474
DeepCCS	[M+Na]+	160.037	30932474
AllCCS	[M+H]+	141.7	32859911
AllCCS	[M+H-H2O]+	137.3	32859911
AllCCS	[M+NH4]+	145.9	32859911
AllCCS	[M+Na]+	147.1	32859911
AllCCS	[M-H]-	141.2	32859911
AllCCS	[M+Na-2H]-	140.8	32859911
AllCCS	[M+HCOO]-	140.3	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Xanthotoxol	[H]OC1=C2OC(=O)C([H])=C([H])C2=C([H])C2=C1OC([H])=C2[H]	3239.7	Standard polar	33892256
Xanthotoxol	[H]OC1=C2OC(=O)C([H])=C([H])C2=C([H])C2=C1OC([H])=C2[H]	1965.0	Standard non polar	33892256
Xanthotoxol	[H]OC1=C2OC(=O)C([H])=C([H])C2=C([H])C2=C1OC([H])=C2[H]	1932.0	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Xanthotoxol,1TMS,isomer #1	C[Si](C)(C)OC1=C2OC=CC2=CC2=C1OC(=O)C=C2	2147.1	Semi standard non polar	33892256
Xanthotoxol,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC1=C2OC=CC2=CC2=C1OC(=O)C=C2	2416.1	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 - Xanthotoxol GC-MS (Non-derivatized) - 70eV, Positive	splash10-0fk9-0920000000-f2a166594cf283c47f5c	2017-07-27	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Xanthotoxol GC-MS (1 TMS) - 70eV, Positive	splash10-00e9-4090000000-dca534ef96e39d848c13	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Xanthotoxol 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 - Xanthotoxol 10V, Positive-QTOF	splash10-0udi-0090000000-c09589cc1f633fd56111	2016-08-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Xanthotoxol 20V, Positive-QTOF	splash10-0udi-0190000000-3ab98291b26fe8eeb4e8	2016-08-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Xanthotoxol 40V, Positive-QTOF	splash10-0pb9-2930000000-4691abe312d6e6ecb939	2016-08-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Xanthotoxol 10V, Negative-QTOF	splash10-0udi-0290000000-c887179a30886be5e421	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Xanthotoxol 20V, Negative-QTOF	splash10-0udi-0390000000-4c461f4a9306d3586bfd	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Xanthotoxol 40V, Negative-QTOF	splash10-0aor-0900000000-b332ff7a37ce35057295	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Xanthotoxol 10V, Positive-QTOF	splash10-0udi-0090000000-2e5a86e101fa40f235c9	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Xanthotoxol 20V, Positive-QTOF	splash10-0udi-0290000000-f0e15e059d45f78f5b76	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Xanthotoxol 40V, Positive-QTOF	splash10-0560-0900000000-5f24b0525848ab617753	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Xanthotoxol 10V, Negative-QTOF	splash10-0udi-0090000000-6f70ceb2368baddf4f40	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Xanthotoxol 20V, Negative-QTOF	splash10-0udi-0090000000-6f70ceb2368baddf4f40	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Xanthotoxol 40V, Negative-QTOF	splash10-0udi-0090000000-1553b0f99d6356baaebd	2021-09-25	Wishart Lab	View Spectrum

IR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M-H]-)	2023-02-03	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)	2023-02-03	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)	2023-02-03	FELIX lab	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm
Extracellular

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

Xanthotoxol

METLIN ID

Not Available

PubChem Compound

65090

PDB ID

Not Available

ChEBI ID

15709

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1037851

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.. .

Enzymes

Enzyme Details

1. UDP-glucuronosyltransferase 1-1

General function:: Involved in transferase activity, transferring hexosyl groups
Specific function:: UDPGT is of major importance in the conjugation and subsequent elimination of potentially toxic xenobiotics and endogenous compounds. This isoform glucuronidates bilirubin IX-alpha to form both the IX-alpha-C8 and IX-alpha-C12 monoconjugates and diconjugate. Is also able to catalyze the glucuronidation of 17beta-estradiol, 17alpha-ethinylestradiol, 1-hydroxypyrene, 4-methylumbelliferone, 1-naphthol, paranitrophenol, scopoletin, and umbelliferone.
Gene Name:: UGT1A1
Uniprot ID:: P22309
Molecular weight:: 59590.91

Reactions

Xanthotoxol → 3,4,5-trihydroxy-6-({7-oxo-7H-furo[3,2-g]chromen-9-yl}oxy)oxane-2-carboxylic acid	details

Showing metabocard for Xanthotoxol (HMDB0029457)

MOL for HMDB0029457 (Xanthotoxol)

3D MOL for HMDB0029457 (Xanthotoxol)

3D SDF for HMDB0029457 (Xanthotoxol)

3D-SDF for HMDB0029457 (Xanthotoxol)

PDB for HMDB0029457 (Xanthotoxol)

3D PDB for HMDB0029457 (Xanthotoxol)

SMILES for HMDB0029457 (Xanthotoxol)

INCHI for HMDB0029457 (Xanthotoxol)

Structure for HMDB0029457 (Xanthotoxol)

3D Structure for HMDB0029457 (Xanthotoxol)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

IR Spectra

Enzymes

Reactions