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Showing metabocard for 2,5-Dimethylthiophene (HMDB0032979)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-11 17:53:03 UTC
Update Date2023-02-21 17:22:55 UTC
HMDB IDHMDB0032979
Secondary Accession Numbers
  • HMDB32979
Metabolite Identification
Common Name2,5-Dimethylthiophene
Description2,5-Dimethylthiophene belongs to the class of organic compounds known as 2,5-disubstituted thiophenes. These are organic compounds containing a thiophene that is disubstituted at the C-2, and C5-positions. 2,5-Dimethylthiophene is a nutty and sulfury tasting compound. 2,5-Dimethylthiophene has been detected, but not quantified in, garden onions (Allium cepa) and soft-necked garlics (Allium sativum L. var. sativum). This could make 2,5-dimethylthiophene a potential biomarker for the consumption of these foods. Based on a literature review a significant number of articles have been published on 2,5-Dimethylthiophene.
Structure
Data?1677000175
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0032979 (2,5-Dimethylthiophene)


  Mrv0541 05061306502D          

  7  7  0  0  0  0            999 V2000
   -0.3297   -0.8227    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.9393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
  4  3  1  0  0  0  0
  5  1  1  0  0  0  0
  5  3  2  0  0  0  0
  6  2  1  0  0  0  0
  6  4  2  0  0  0  0
  7  5  1  0  0  0  0
  7  6  1  0  0  0  0
M  END
Download

3D MOL for HMDB0032979 (2,5-Dimethylthiophene)

HMDB0032979
     RDKit          3D
2,5-Dimethylthiophene
 15 15  0  0  0  0  0  0  0  0999 V2000
    2.7464    0.5870   -0.0450 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2803    0.2381   -0.0223 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7208   -1.0146    0.0014 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6254   -1.0764    0.0186 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3122    0.0974    0.0112 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7873    0.3496    0.0258 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0777    1.2703   -0.0197 S   0  0  0  0  0  0  0  0  0  0  0  0
    2.8073    1.5987    0.4113 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1039    0.6903   -1.0808 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3160   -0.1106    0.5707 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4039   -1.9026    0.0050 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1701   -2.0387    0.0383 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3109   -0.6130    0.0196 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0094    0.9899   -0.8576 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0856    0.9348    0.9234 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
  5  6  1  0
  5  7  1  0
  7  2  1  0
  1  8  1  0
  1  9  1  0
  1 10  1  0
  3 11  1  0
  4 12  1  0
  6 13  1  0
  6 14  1  0
  6 15  1  0
M  END
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3D SDF for HMDB0032979 (2,5-Dimethylthiophene)


  Mrv0541 05061306502D          

  7  7  0  0  0  0            999 V2000
   -0.3297   -0.8227    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.9393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
  4  3  1  0  0  0  0
  5  1  1  0  0  0  0
  5  3  2  0  0  0  0
  6  2  1  0  0  0  0
  6  4  2  0  0  0  0
  7  5  1  0  0  0  0
  7  6  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0032979

> <DATABASE_NAME>
hmdb

> <SMILES>
CC1=CC=C(C)S1

> <INCHI_IDENTIFIER>
InChI=1S/C6H8S/c1-5-3-4-6(2)7-5/h3-4H,1-2H3

> <INCHI_KEY>
GWQOOADXMVQEFT-UHFFFAOYSA-N

> <FORMULA>
C6H8S

> <MOLECULAR_WEIGHT>
112.193

> <EXACT_MASS>
112.034670946

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_AVERAGE_POLARIZABILITY>
12.785524289865458

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2,5-dimethylthiophene

> <ALOGPS_LOGP>
2.71

> <JCHEM_LOGP>
3.0454093876666666

> <ALOGPS_LOGS>
-2.32

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-7.0084850693165395

> <JCHEM_POLAR_SURFACE_AREA>
0

> <JCHEM_REFRACTIVITY>
33.2764

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.32e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2,5-dimethylthiophene

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0032979 (2,5-Dimethylthiophene)

HMDB0032979
     RDKit          3D
2,5-Dimethylthiophene
 15 15  0  0  0  0  0  0  0  0999 V2000
    2.7464    0.5870   -0.0450 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2803    0.2381   -0.0223 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7208   -1.0146    0.0014 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6254   -1.0764    0.0186 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3122    0.0974    0.0112 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7873    0.3496    0.0258 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0777    1.2703   -0.0197 S   0  0  0  0  0  0  0  0  0  0  0  0
    2.8073    1.5987    0.4113 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1039    0.6903   -1.0808 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3160   -0.1106    0.5707 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4039   -1.9026    0.0050 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1701   -2.0387    0.0383 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3109   -0.6130    0.0196 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0094    0.9899   -0.8576 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0856    0.9348    0.9234 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
  5  6  1  0
  5  7  1  0
  7  2  1  0
  1  8  1  0
  1  9  1  0
  1 10  1  0
  3 11  1  0
  4 12  1  0
  6 13  1  0
  6 14  1  0
  6 15  1  0
M  END
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PDB for HMDB0032979 (2,5-Dimethylthiophene)

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      -0.615  -1.536   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.060   3.620   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.830  -0.290   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.306   1.175   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.290  -0.290   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.060   2.080   0.000  0.00  0.00           C+0
HETATM    7  S   UNK     0      -0.186   1.175   0.000  0.00  0.00           S+0
CONECT    1    5                                                            
CONECT    2    6                                                            
CONECT    3    4    5                                                       
CONECT    4    3    6                                                       
CONECT    5    1    3    7                                                  
CONECT    6    2    4    7                                                  
CONECT    7    5    6                                                       
MASTER        0    0    0    0    0    0    0    0    7    0   14    0
END
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3D PDB for HMDB0032979 (2,5-Dimethylthiophene)

COMPND    HMDB0032979
HETATM    1  C1  UNL     1       2.746   0.587  -0.045  1.00  0.00           C  
HETATM    2  C2  UNL     1       1.280   0.238  -0.022  1.00  0.00           C  
HETATM    3  C3  UNL     1       0.721  -1.015   0.001  1.00  0.00           C  
HETATM    4  C4  UNL     1      -0.625  -1.076   0.019  1.00  0.00           C  
HETATM    5  C5  UNL     1      -1.312   0.097   0.011  1.00  0.00           C  
HETATM    6  C6  UNL     1      -2.787   0.350   0.026  1.00  0.00           C  
HETATM    7  S1  UNL     1      -0.078   1.270  -0.020  1.00  0.00           S  
HETATM    8  H1  UNL     1       2.807   1.599   0.411  1.00  0.00           H  
HETATM    9  H2  UNL     1       3.104   0.690  -1.081  1.00  0.00           H  
HETATM   10  H3  UNL     1       3.316  -0.111   0.571  1.00  0.00           H  
HETATM   11  H4  UNL     1       1.404  -1.903   0.005  1.00  0.00           H  
HETATM   12  H5  UNL     1      -1.170  -2.039   0.038  1.00  0.00           H  
HETATM   13  H6  UNL     1      -3.311  -0.613   0.020  1.00  0.00           H  
HETATM   14  H7  UNL     1      -3.009   0.990  -0.858  1.00  0.00           H  
HETATM   15  H8  UNL     1      -3.086   0.935   0.923  1.00  0.00           H  
CONECT    1    2    8    9   10
CONECT    2    3    3    7
CONECT    3    4   11
CONECT    4    5    5   12
CONECT    5    6    7
CONECT    6   13   14   15
END
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SMILES for HMDB0032979 (2,5-Dimethylthiophene)

CC1=CC=C(C)S1
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INCHI for HMDB0032979 (2,5-Dimethylthiophene)

InChI=1S/C6H8S/c1-5-3-4-6(2)7-5/h3-4H,1-2H3
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View in JSmolView Stereo Labels
Synonyms
ValueSource
2,5-Dimethyl-thiopheneHMDB
Chemical FormulaC6H8S
Average Molecular Weight112.193
Monoisotopic Molecular Weight112.034670946
IUPAC Name2,5-dimethylthiophene
Traditional Name2,5-dimethylthiophene
CAS Registry Number638-02-8
SMILES
CC1=CC=C(C)S1
InChI Identifier
InChI=1S/C6H8S/c1-5-3-4-6(2)7-5/h3-4H,1-2H3
InChI KeyGWQOOADXMVQEFT-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as 2,5-disubstituted thiophenes. These are organic compounds containing a thiophene that is disubstituted at the C-2, and C5-positions.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassThiophenes
Sub Class2,5-disubstituted thiophenes
Direct Parent2,5-disubstituted thiophenes
Alternative Parents
Substituents
  • 2,5-disubstituted thiophene
  • Heteroaromatic compound
  • Hydrocarbon derivative
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Physiological effect
Organoleptic effect
Disposition
Biological locationRoute of exposureSource
ProcessNot Available
Role
Biological role
Physical Properties
StateLiquid
Experimental Molecular Properties
PropertyValueReference
Melting Point-62.6 °CNot Available
Boiling Point135.00 °C. @ 760.00 mm HgThe Good Scents Company Information System
Water Solubility351.5 mg/L @ 25 °C (est)The Good Scents Company Information System
LogP2.523 (est)The Good Scents Company Information System
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility0.53 g/LALOGPS
logP2.71ALOGPS
logP3.05ChemAxon
logS-2.3ALOGPS
pKa (Strongest Basic)-7ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count0ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area0 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity33.28 m³·mol⁻¹ChemAxon
Polarizability12.79 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+120.45331661259
DarkChem[M-H]-115.91631661259
DeepCCS[M+H]+132.01230932474
DeepCCS[M-H]-129.86730932474
DeepCCS[M-2H]-165.60530932474
DeepCCS[M+Na]+140.49230932474
AllCCS[M+H]+116.432859911
AllCCS[M+H-H2O]+111.532859911
AllCCS[M+NH4]+121.132859911
AllCCS[M+Na]+122.432859911
AllCCS[M-H]-121.032859911
AllCCS[M+Na-2H]-124.032859911
AllCCS[M+HCOO]-127.432859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
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. 4.32 minutes32390414
Predicted by Siyang on May 30, 202216.071 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20222.23 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid1800.9 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid648.5 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid252.7 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid449.5 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid298.1 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid561.4 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid608.3 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)309.5 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid1277.4 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid492.7 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid1375.5 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid474.4 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid385.0 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate569.8 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA469.8 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water66.8 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
2,5-DimethylthiopheneCC1=CC=C(C)S11178.3Standard polar33892256
2,5-DimethylthiopheneCC1=CC=C(C)S1861.4Standard non polar33892256
2,5-DimethylthiopheneCC1=CC=C(C)S1877.6Semi standard non polar33892256
Spectra
Biological Properties
Cellular Locations
  • Membrane
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB010966
KNApSAcK IDNot Available
Chemspider ID11998
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia Link2,5-Dimethylthiophene
METLIN IDNot Available
PubChem Compound12514
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1043071
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. (). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .