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Showing metabocard for Thymoquinone (HMDB0034732)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2012-09-11 19:38:04 UTC
Update Date2023-02-21 17:24:21 UTC
HMDB IDHMDB0034732
Secondary Accession Numbers
  • HMDB34732
Metabolite Identification
Common NameThymoquinone
DescriptionThymoquinone, 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
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0034732 (Thymoquinone)

  Mrv0541 05061308022D          

 12 12  0  0  0  0            999 V2000
    1.4289   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    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
    0.0000    0.0000    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
    0.7145    1.2375    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
    1.4289    0.0000    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   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  6  1  1  0  0  0  0
  6  2  1  0  0  0  0
  7  3  1  0  0  0  0
  7  4  2  0  0  0  0
  8  5  2  0  0  0  0
  8  6  1  0  0  0  0
  9  5  1  0  0  0  0
  9  7  1  0  0  0  0
 10  4  1  0  0  0  0
 10  8  1  0  0  0  0
 11  9  2  0  0  0  0
 12 10  2  0  0  0  0
M  END
Download

3D MOL for HMDB0034732 (Thymoquinone)

HMDB0034732
     RDKit          3D
Thymoquinone
 24 24  0  0  0  0  0  0  0  0999 V2000
    3.8853   -0.3536    0.0124 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4119   -0.1261    0.0240 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8288    0.6704    0.9053 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3848    0.8858    0.9073 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1644    1.6574    1.7640 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4929    0.2360   -0.0605 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9585    0.4674   -0.0432 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6703   -0.1479   -1.1960 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5937    0.0491    1.2660 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0946   -0.5592   -0.9395 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5359   -0.7755   -0.9430 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0828   -1.5470   -1.8001 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4317    0.5031    0.4625 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1728   -1.2952    0.5101 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2686   -0.4179   -1.0455 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4689    1.1631    1.6344 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1255    1.5770   -0.1211 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7384    0.1493   -1.1316 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6576   -1.2519   -1.2080 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2992    0.2547   -2.1579 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3705    0.7854    1.5839 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8352    0.0450    2.0681 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1207   -0.9219    1.1710 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5391   -1.0477   -1.6622 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  4  6  1  0
  6  7  1  0
  7  8  1  0
  7  9  1  0
  6 10  2  0
 10 11  1  0
 11 12  2  0
 11  2  1  0
  1 13  1  0
  1 14  1  0
  1 15  1  0
  3 16  1  0
  7 17  1  0
  8 18  1  0
  8 19  1  0
  8 20  1  0
  9 21  1  0
  9 22  1  0
  9 23  1  0
 10 24  1  0
M  END
Download

3D SDF for HMDB0034732 (Thymoquinone)

  Mrv0541 05061308022D          

 12 12  0  0  0  0            999 V2000
    1.4289   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    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
    0.0000    0.0000    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
    0.7145    1.2375    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
    1.4289    0.0000    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   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  6  1  1  0  0  0  0
  6  2  1  0  0  0  0
  7  3  1  0  0  0  0
  7  4  2  0  0  0  0
  8  5  2  0  0  0  0
  8  6  1  0  0  0  0
  9  5  1  0  0  0  0
  9  7  1  0  0  0  0
 10  4  1  0  0  0  0
 10  8  1  0  0  0  0
 11  9  2  0  0  0  0
 12 10  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0034732

> <DATABASE_NAME>
hmdb

> <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

> <FORMULA>
C10H12O2

> <MOLECULAR_WEIGHT>
164.2011

> <EXACT_MASS>
164.083729628

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_AVERAGE_POLARIZABILITY>
17.83827252327761

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

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

> <ALOGPS_LOGP>
2.00

> <JCHEM_LOGP>
2.546802551333333

> <ALOGPS_LOGS>
-1.95

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-7.74622466426713

> <JCHEM_POLAR_SURFACE_AREA>
34.14

> <JCHEM_REFRACTIVITY>
48.89260000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.83e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
thymoquinone

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0034732 (Thymoquinone)

HMDB0034732
     RDKit          3D
Thymoquinone
 24 24  0  0  0  0  0  0  0  0999 V2000
    3.8853   -0.3536    0.0124 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4119   -0.1261    0.0240 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8288    0.6704    0.9053 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3848    0.8858    0.9073 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1644    1.6574    1.7640 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4929    0.2360   -0.0605 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9585    0.4674   -0.0432 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6703   -0.1479   -1.1960 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5937    0.0491    1.2660 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0946   -0.5592   -0.9395 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5359   -0.7755   -0.9430 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0828   -1.5470   -1.8001 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4317    0.5031    0.4625 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1728   -1.2952    0.5101 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2686   -0.4179   -1.0455 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4689    1.1631    1.6344 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1255    1.5770   -0.1211 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7384    0.1493   -1.1316 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6576   -1.2519   -1.2080 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2992    0.2547   -2.1579 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3705    0.7854    1.5839 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8352    0.0450    2.0681 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1207   -0.9219    1.1710 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5391   -1.0477   -1.6622 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  4  6  1  0
  6  7  1  0
  7  8  1  0
  7  9  1  0
  6 10  2  0
 10 11  1  0
 11 12  2  0
 11  2  1  0
  1 13  1  0
  1 14  1  0
  1 15  1  0
  3 16  1  0
  7 17  1  0
  8 18  1  0
  8 19  1  0
  8 20  1  0
  9 21  1  0
  9 22  1  0
  9 23  1  0
 10 24  1  0
M  END
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PDB for HMDB0034732 (Thymoquinone)

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
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3D PDB for HMDB0034732 (Thymoquinone)

COMPND    HMDB0034732
HETATM    1  C1  UNL     1       3.885  -0.354   0.012  1.00  0.00           C  
HETATM    2  C2  UNL     1       2.412  -0.126   0.024  1.00  0.00           C  
HETATM    3  C3  UNL     1       1.829   0.670   0.905  1.00  0.00           C  
HETATM    4  C4  UNL     1       0.385   0.886   0.907  1.00  0.00           C  
HETATM    5  O1  UNL     1      -0.164   1.657   1.764  1.00  0.00           O  
HETATM    6  C5  UNL     1      -0.493   0.236  -0.060  1.00  0.00           C  
HETATM    7  C6  UNL     1      -1.958   0.467  -0.043  1.00  0.00           C  
HETATM    8  C7  UNL     1      -2.670  -0.148  -1.196  1.00  0.00           C  
HETATM    9  C8  UNL     1      -2.594   0.049   1.266  1.00  0.00           C  
HETATM   10  C9  UNL     1       0.095  -0.559  -0.940  1.00  0.00           C  
HETATM   11  C10 UNL     1       1.536  -0.775  -0.943  1.00  0.00           C  
HETATM   12  O2  UNL     1       2.083  -1.547  -1.800  1.00  0.00           O  
HETATM   13  H1  UNL     1       4.432   0.503   0.463  1.00  0.00           H  
HETATM   14  H2  UNL     1       4.173  -1.295   0.510  1.00  0.00           H  
HETATM   15  H3  UNL     1       4.269  -0.418  -1.046  1.00  0.00           H  
HETATM   16  H4  UNL     1       2.469   1.163   1.634  1.00  0.00           H  
HETATM   17  H5  UNL     1      -2.125   1.577  -0.121  1.00  0.00           H  
HETATM   18  H6  UNL     1      -3.738   0.149  -1.132  1.00  0.00           H  
HETATM   19  H7  UNL     1      -2.658  -1.252  -1.208  1.00  0.00           H  
HETATM   20  H8  UNL     1      -2.299   0.255  -2.158  1.00  0.00           H  
HETATM   21  H9  UNL     1      -3.370   0.785   1.584  1.00  0.00           H  
HETATM   22  H10 UNL     1      -1.835   0.045   2.068  1.00  0.00           H  
HETATM   23  H11 UNL     1      -3.121  -0.922   1.171  1.00  0.00           H  
HETATM   24  H12 UNL     1      -0.539  -1.048  -1.662  1.00  0.00           H  
CONECT    1    2   13   14   15
CONECT    2    3    3   11
CONECT    3    4   16
CONECT    4    5    5    6
CONECT    6    7   10   10
CONECT    7    8    9   17
CONECT    8   18   19   20
CONECT    9   21   22   23
CONECT   10   11   24
CONECT   11   12   12
END
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SMILES for HMDB0034732 (Thymoquinone)

CC(C)C1=CC(=O)C(C)=CC1=O
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INCHI for HMDB0034732 (Thymoquinone)

InChI=1S/C10H12O2/c1-6(2)8-5-9(11)7(3)4-10(8)12/h4-6H,1-3H3
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
Chemical FormulaC10H12O2
Average Molecular Weight164.2011
Monoisotopic Molecular Weight164.083729628
IUPAC Name2-methyl-5-(propan-2-yl)cyclohexa-2,5-diene-1,4-dione
Traditional Namethymoquinone
CAS Registry Number490-91-5
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 KeyKEQHJBNSCLWCAE-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.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbonyl compounds
Direct ParentP-benzoquinones
Alternative Parents
Substituents
  • P-benzoquinone
  • Organic oxide
  • Hydrocarbon derivative
  • Aliphatic homomonocyclic compound
Molecular FrameworkAliphatic homomonocyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological locationRoute of exposureSource
Process
Naturally occurring process
Role
Industrial applicationBiological role
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point44 - 45 °CNot Available
Boiling Point230.00 to 232.00 °C. @ 760.00 mm HgThe Good Scents Company Information System
Water Solubility865.3 mg/L @ 25 °C (est)The Good Scents Company Information System
LogP2.20Not Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
  • Membrane
Biospecimen Locations
  • Blood
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedCancer patients undergoing total body irradiation details
UrineDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedCancer patients undergoing total body irradiation details
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB013274
KNApSAcK IDC00010876
Chemspider ID9861
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkThymoquinone
METLIN IDNot Available
PubChem Compound10281
PDB IDIMW
ChEBI ID113532
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1289381
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. 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 ]
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