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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2012-09-11 19:38:04 UTC

Update Date

2023-02-21 17:24:21 UTC

HMDB ID

HMDB0034732

Secondary Accession Numbers

HMDB34732

Metabolite Identification

Common Name

Thymoquinone

Description

Thymoquinone, also known as TQ, belongs to the class of organic compounds known as p-benzoquinones. These are benzoquinones where the two C=O groups are attached at the 1- and 4-positions, respectively. Thymoquinone is found, on average, in the highest concentration within winter savories (Satureja montana). Thymoquinone has also been detected, but not quantified in, herbs and spices. This could make thymoquinone a potential biomarker for the consumption of these foods. Thymoquinone is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. Based on a literature review a significant number of articles have been published on Thymoquinone.

Structure

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

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  -3.080   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000  -3.080   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -1.334   2.310   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       4.001  -0.770   0.000  0.00  0.00           O+0
CONECT    1    6                                                            
CONECT    2    6                                                            
CONECT    3    7                                                            
CONECT    4    7   10                                                       
CONECT    5    8    9                                                       
CONECT    6    1    2    8                                                  
CONECT    7    3    4    9                                                  
CONECT    8    5    6   10                                                  
CONECT    9    5    7   11                                                  
CONECT   10    4    8   12                                                  
CONECT   11    9                                                            
CONECT   12   10                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   24    0
END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
2-Isopropyl-5-methyl-1,4-benzoquinone	ChEBI
2-Isopropyl-5-methyl-p-benzoquinone	ChEBI
2-Methyl-5-(1-methylethyl)-2,5-cyclohexadiene-1,4-dione	ChEBI
5-Isopropyl-2-methyl-2,5-cyclohexadiene-1,4-dione	ChEBI
p-Cymene-2,5-dione	ChEBI
p-Mentha-3,6-diene-2,5-dione	ChEBI
Thymoquinon	ChEBI
TQ	ChEBI
2-Isopropyl-5-methylbenzo-1,4-quinone	HMDB
2-Isopropyl-5-methylbenzoquinone	HMDB, MeSH
2-Methyl-5-(1-methylethyl)-2,5-cyclohexadiene-1,4-dione, 9ci	HMDB
2-Methyl-5-isopropyl-1,4-benzoquinone	HMDB
2-Methyl-5-isopropyl-P-benzoquinone	HMDB, MeSH
5-Isopropyl-2-methyl-1,4-benzoquinone	HMDB
5-Isopropyl-2-methyl-P-benzoquinone	HMDB
P-Mentha-3,6-diene-2,5-dione (8ci)	HMDB
Polythymoquinone	HMDB
Thymoil	HMDB
Thymolquinone	HMDB
Dihydrothymoquinone	MeSH, HMDB
Thymoquinone	MeSH

Chemical Formula

C₁₀H₁₂O₂

Average Molecular Weight

164.2011

Monoisotopic Molecular Weight

164.083729628

IUPAC Name

2-methyl-5-(propan-2-yl)cyclohexa-2,5-diene-1,4-dione

Traditional Name

thymoquinone

CAS Registry Number

490-91-5

SMILES

CC(C)C1=CC(=O)C(C)=CC1=O

InChI Identifier

InChI=1S/C10H12O2/c1-6(2)8-5-9(11)7(3)4-10(8)12/h4-6H,1-3H3

InChI Key

KEQHJBNSCLWCAE-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as p-benzoquinones. These are benzoquinones where the two C=O groups are attached at the 1- and 4-positions, respectively.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbonyl compounds

Direct Parent

P-benzoquinones

Alternative Parents

Substituents

P-benzoquinone
Organic oxide
Hydrocarbon derivative
Aliphatic homomonocyclic compound

Molecular Framework

Aliphatic homomonocyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Route of exposure

Enteral

Ingestion (HMDB: HMDB0034732)

Source

Exogenous

Exogenous (HMDB: HMDB0034732)

Food

Food (HMDB: HMDB0034732)

Herb and spice

Herb

Winter savory (FooDB: FOOD00168)

Herbs and Spices (FooDB: FOOD00866)

Endogenous

Endogenous (HMDB: HMDB0034732)

Plant

Plant (HMDB: HMDB0034732)

Process

Naturally occurring process

Biological process

Cellular process

Cell signaling (HMDB: HMDB0034732)

Role

Industrial applicationBiological role

Modulator

Inhibitor

EC 1.14.99.1 (prostaglandin-endoperoxide synthase) inhibitor (HMDB: HMDB0034732)

Enzyme inhibitor

Lipoxygenase inhibitor (HMDB: HMDB0034732)
Cyclooxygenase inhibitor (HMDB: HMDB0034732)

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	44 - 45 °C	Not Available
Boiling Point	230.00 to 232.00 °C. @ 760.00 mm Hg	The Good Scents Company Information System
Water Solubility	865.3 mg/L @ 25 °C (est)	The Good Scents Company Information System
LogP	2.20	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	1.83 g/L	ALOGPS
logP	2	ALOGPS
logP	2.55	ChemAxon
logS	-2	ALOGPS
pKa (Strongest Basic)	-7.7	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	34.14 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	48.89 m³·mol⁻¹	ChemAxon
Polarizability	17.84 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	138.216	31661259
DarkChem	[M-H]-	132.773	31661259
DeepCCS	[M+H]+	138.44	30932474
DeepCCS	[M-H]-	134.613	30932474
DeepCCS	[M-2H]-	172.106	30932474
DeepCCS	[M+Na]+	147.645	30932474
AllCCS	[M+H]+	133.9	32859911
AllCCS	[M+H-H2O]+	129.5	32859911
AllCCS	[M+NH4]+	138.0	32859911
AllCCS	[M+Na]+	139.2	32859911
AllCCS	[M-H]-	137.0	32859911
AllCCS	[M+Na-2H]-	138.1	32859911
AllCCS	[M+HCOO]-	139.5	32859911

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.	6.1 minutes	32390414
Predicted by Siyang on May 30, 2022	12.19 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	0.74 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	1712.7 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	393.9 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	143.0 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	229.2 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	65.2 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	460.9 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	523.0 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	65.9 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	896.0 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	373.5 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	1277.3 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	283.9 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	317.0 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	389.5 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	372.9 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	35.7 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Thymoquinone	CC(C)C1=CC(=O)C(C)=CC1=O	1916.6	Standard polar	33892256
Thymoquinone	CC(C)C1=CC(=O)C(C)=CC1=O	1239.4	Standard non polar	33892256
Thymoquinone	CC(C)C1=CC(=O)C(C)=CC1=O	1230.2	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 - Thymoquinone GC-MS (Non-derivatized) - 70eV, Positive	splash10-00xr-6900000000-764f3b8a1150b1cac052	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Thymoquinone GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Thymoquinone 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 - Thymoquinone 10V, Positive-QTOF	splash10-014i-0900000000-96f0c8e4e4f4a8455abe	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Thymoquinone 20V, Positive-QTOF	splash10-014i-5900000000-441064ba80ff42a70cfe	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Thymoquinone 40V, Positive-QTOF	splash10-014i-9200000000-c6d527c2a9a79f901029	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Thymoquinone 10V, Negative-QTOF	splash10-03di-0900000000-d9e63c8d82efebaf41b1	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Thymoquinone 20V, Negative-QTOF	splash10-03di-0900000000-98b2dccaab2bbdb236fe	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Thymoquinone 40V, Negative-QTOF	splash10-014r-9500000000-19dae31b3a18d5f7735c	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Thymoquinone 10V, Negative-QTOF	splash10-03di-0900000000-8db47caa9667c101bd0f	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Thymoquinone 20V, Negative-QTOF	splash10-03di-0900000000-5a485fdf30f3fb6eef66	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Thymoquinone 40V, Negative-QTOF	splash10-014i-9500000000-e6c8bd2fffd875c29cff	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Thymoquinone 10V, Positive-QTOF	splash10-014i-0900000000-7a4cd3c2c5dcf8576412	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Thymoquinone 20V, Positive-QTOF	splash10-00xr-3900000000-c1e3ac1b0edf80cd5e27	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Thymoquinone 40V, Positive-QTOF	splash10-00kf-9100000000-897472ebb650188b991d	2021-09-24	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	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]+)	2023-02-04	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)	2023-02-04	FELIX lab	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm
Extracellular
Membrane

Biospecimen Locations

Blood
Urine

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

Abnormal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Cancer patients undergoing total body irradiation	31424920	details
Urine	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Cancer patients undergoing total body irradiation	31424920	details

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

FDB013274

KNApSAcK ID

C00010876

Chemspider ID

9861

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Thymoquinone

METLIN ID

Not Available

PubChem Compound

10281

PDB ID

IMW

ChEBI ID

113532

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1289381

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Reindl W, Yuan J, Kramer A, Strebhardt K, Berg T: Inhibition of polo-like kinase 1 by blocking polo-box domain-dependent protein-protein interactions. Chem Biol. 2008 May;15(5):459-66. doi: 10.1016/j.chembiol.2008.03.013. [PubMed:18482698 ]
Fararh KM, Shimizu Y, Shiina T, Nikami H, Ghanem MM, Takewaki T: Thymoquinone reduces hepatic glucose production in diabetic hamsters. Res Vet Sci. 2005 Dec;79(3):219-23. Epub 2005 Apr 1. [PubMed:16054891 ]
Abdel-Fattah AM, Matsumoto K, Watanabe H: Antinociceptive effects of Nigella sativa oil and its major component, thymoquinone, in mice. Eur J Pharmacol. 2000 Jul 14;400(1):89-97. [PubMed:10913589 ]
Hosseinzadeh H, Parvardeh S: Anticonvulsant effects of thymoquinone, the major constituent of Nigella sativa seeds, in mice. Phytomedicine. 2004 Jan;11(1):56-64. [PubMed:14971722 ]
(). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .

Showing metabocard for Thymoquinone (HMDB0034732)

MOL for HMDB0034732 (Thymoquinone)

3D MOL for HMDB0034732 (Thymoquinone)

3D SDF for HMDB0034732 (Thymoquinone)

3D-SDF for HMDB0034732 (Thymoquinone)

PDB for HMDB0034732 (Thymoquinone)

3D PDB for HMDB0034732 (Thymoquinone)

SMILES for HMDB0034732 (Thymoquinone)

INCHI for HMDB0034732 (Thymoquinone)

Structure for HMDB0034732 (Thymoquinone)

3D Structure for HMDB0034732 (Thymoquinone)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

IR Spectra