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Showing metabocard for Thiophene (HMDB0029718)

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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2012-09-11 17:32:14 UTC
Update Date2023-02-21 17:19:07 UTC
HMDB IDHMDB0029718
Secondary Accession Numbers
  • HMDB29718
Metabolite Identification
Common NameThiophene
DescriptionThiophene is a maillard product. At room temperature, thiophene is a colorless liquid with a mildly pleasant odor reminiscent of benzene, with which thiophene shares some similarities. The high reactivity of thiophene toward sulfonation is the basis for the separation of thiophene from benzene, which are difficult to separate by distillation due to their similar boiling points (4 °C difference at ambient pressure). Like benzene, thiophene forms an azeotrope with water. Not only is thiophene reactive toward electrophiles, it is also readily lithiated with butyl lithium to give 2-lithiothiophene, which is a precursor to a variety of derivatives, including dithienyl
Structure
Data?1676999946
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0029718 (Thiophene)


  Mrv1652305271900302D          

  5  5  0  0  0  0            999 V2000
   -0.6191    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2059    0.6605    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.6191    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2059   -0.6605    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6191   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  5  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
M  END
Download

3D MOL for HMDB0029718 (Thiophene)

HMDB0029718
     RDKit          3D
Thiophene
  9  9  0  0  0  0  0  0  0  0999 V2000
    0.6775   -0.6220    0.0209 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6673   -0.6206    0.0820 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2996    0.5916    0.0100 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0047    1.6860   -0.1400 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.2985    0.5956   -0.1087 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2663   -1.5768    0.0735 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2517   -1.5705    0.1876 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3926    0.7436    0.0471 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3737    0.7731   -0.1724 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  1  0
  5  1  2  0
  1  6  1  0
  2  7  1  0
  3  8  1  0
  5  9  1  0
M  END
Download

3D SDF for HMDB0029718 (Thiophene)


  Mrv1652305271900302D          

  5  5  0  0  0  0            999 V2000
   -0.6191    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2059    0.6605    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.6191    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2059   -0.6605    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6191   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  5  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0029718

> <DATABASE_NAME>
hmdb

> <SMILES>
S1C=CC=C1

> <INCHI_IDENTIFIER>
InChI=1S/C4H4S/c1-2-4-5-3-1/h1-4H

> <INCHI_KEY>
YTPLMLYBLZKORZ-UHFFFAOYSA-N

> <FORMULA>
C4H4S

> <MOLECULAR_WEIGHT>
84.14

> <EXACT_MASS>
84.003370818

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_ATOM_COUNT>
9

> <JCHEM_AVERAGE_POLARIZABILITY>
8.55734014130827

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
thiophene

> <ALOGPS_LOGP>
1.89

> <JCHEM_LOGP>
1.753687769

> <ALOGPS_LOGS>
-1.84

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_POLAR_SURFACE_AREA>
0.0

> <JCHEM_REFRACTIVITY>
23.1638

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.22e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
thiophene

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0029718 (Thiophene)

HMDB0029718
     RDKit          3D
Thiophene
  9  9  0  0  0  0  0  0  0  0999 V2000
    0.6775   -0.6220    0.0209 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6673   -0.6206    0.0820 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2996    0.5916    0.0100 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0047    1.6860   -0.1400 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.2985    0.5956   -0.1087 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2663   -1.5768    0.0735 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2517   -1.5705    0.1876 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3926    0.7436    0.0471 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3737    0.7731   -0.1724 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  1  0
  5  1  2  0
  1  6  1  0
  2  7  1  0
  3  8  1  0
  5  9  1  0
M  END
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PDB for HMDB0029718 (Thiophene)

HEADER    PROTEIN                                 27-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-MAY-19         0                                  
HETATM    1  C   UNK     0      -1.156   0.770   0.000  0.00  0.00           C+0
HETATM    2  S   UNK     0       0.384   1.233   0.000  0.00  0.00           S+0
HETATM    3  C   UNK     0       1.156   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.384  -1.233   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -1.156  -0.770   0.000  0.00  0.00           C+0
CONECT    1    2    5                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    1    4                                                       
MASTER        0    0    0    0    0    0    0    0    5    0   10    0
END
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3D PDB for HMDB0029718 (Thiophene)

COMPND    HMDB0029718
HETATM    1  C1  UNL     1       0.678  -0.622   0.021  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.667  -0.621   0.082  1.00  0.00           C  
HETATM    3  C3  UNL     1      -1.300   0.592   0.010  1.00  0.00           C  
HETATM    4  S1  UNL     1      -0.005   1.686  -0.140  1.00  0.00           S  
HETATM    5  C4  UNL     1       1.298   0.596  -0.109  1.00  0.00           C  
HETATM    6  H1  UNL     1       1.266  -1.577   0.073  1.00  0.00           H  
HETATM    7  H2  UNL     1      -1.252  -1.570   0.188  1.00  0.00           H  
HETATM    8  H3  UNL     1      -2.393   0.744   0.047  1.00  0.00           H  
HETATM    9  H4  UNL     1       2.374   0.773  -0.172  1.00  0.00           H  
CONECT    1    2    5    5    6
CONECT    2    3    3    7
CONECT    3    4    8
CONECT    4    5
CONECT    5    9
END
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SMILES for HMDB0029718 (Thiophene)

S1C=CC=C1
Download

INCHI for HMDB0029718 (Thiophene)

InChI=1S/C4H4S/c1-2-4-5-3-1/h1-4H
Download
View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
ThiofuranChEBI
ThiophenChEBI
ThiophenesMeSH
2-Thienylacetic acidHMDB
2-Thiopheneacetic acidHMDB
Divinylene sulfideHMDB
Hopkin'S lactic acid reagentHMDB
PolythiopheneHMDB
ThiacyclopentadieneHMDB
ThiapheneHMDB
Thien-2-ylacetateHMDB
thio-FuranHMDB
ThiofenHMDB
ThiofuramHMDB
ThiofurfuranHMDB
ThioleHMDB
Thiophene, homopolymerHMDB
ThiotetroleHMDB
Chemical FormulaC4H4S
Average Molecular Weight84.14
Monoisotopic Molecular Weight84.003370818
IUPAC Namethiophene
Traditional Namethiophene
CAS Registry Number110-02-1
SMILES
S1C=CC=C1
InChI Identifier
InChI=1S/C4H4S/c1-2-4-5-3-1/h1-4H
InChI KeyYTPLMLYBLZKORZ-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as heteroaromatic compounds. Heteroaromatic compounds are compounds containing an aromatic ring where a carbon atom is linked to an hetero atom.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassHeteroaromatic compounds
Sub ClassNot Available
Direct ParentHeteroaromatic compounds
Alternative Parents
Substituents
  • Heteroaromatic compound
  • Thiophene
  • Hydrocarbon derivative
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effect
Organoleptic effect
Disposition
Biological locationSource
ProcessNot Available
Role
Industrial applicationBiological role
Physical Properties
StateLiquid
Experimental Molecular Properties
PropertyValueReference
Melting Point-38.3 °CNot Available
Boiling Point84.00 °C. @ 760.00 mm HgThe Good Scents Company Information System
Water Solubility3.01 mg/mL at 25 °CNot Available
LogP1.81Not Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility1.22 g/LALOGPS
logP1.89ALOGPS
logP1.75ChemAxon
logS-1.8ALOGPS
Physiological Charge0ChemAxon
Hydrogen Acceptor Count0ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area0 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity23.16 m³·mol⁻¹ChemAxon
Polarizability8.56 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]+110.34631661259
DarkChem[M-H]-104.21731661259
DeepCCS[M+H]+118.8430932474
DeepCCS[M-H]-116.52530932474
DeepCCS[M-2H]-152.47830932474
DeepCCS[M+Na]+127.02930932474
AllCCS[M+H]+113.732859911
AllCCS[M+H-H2O]+108.432859911
AllCCS[M+NH4]+118.732859911
AllCCS[M+Na]+120.132859911
AllCCS[M-H]-120.732859911
AllCCS[M+Na-2H]-125.232859911
AllCCS[M+HCOO]-130.132859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
ThiopheneS1C=CC=C11005.2Standard polar33892256
ThiopheneS1C=CC=C1631.8Standard non polar33892256
ThiopheneS1C=CC=C1685.0Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Thiophene GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Thiophene GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Thiophene 10V, Positive-QTOFsplash10-000i-9000000000-b617a94704f7b42da42d2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Thiophene 20V, Positive-QTOFsplash10-000i-9000000000-c293c7cf614468c6e0e42016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Thiophene 40V, Positive-QTOFsplash10-0udr-9000000000-9a03d6e6508f838823342016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Thiophene 10V, Negative-QTOFsplash10-001i-9000000000-052f8b82aca4fcb7d7152016-08-04Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Thiophene 20V, Negative-QTOFsplash10-001i-9000000000-3b6cb97c53d937e7660a2016-08-04Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Thiophene 40V, Negative-QTOFsplash10-0a59-9000000000-67fd3ae2e7363f5336a52016-08-04Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Thiophene 10V, Positive-QTOFsplash10-000i-9000000000-50012c27a822f42837d12021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Thiophene 20V, Positive-QTOFsplash10-000i-9000000000-9302853ffcaa63f5c40d2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Thiophene 40V, Positive-QTOFsplash10-000i-9000000000-03bd3cb32a613ac4d5e72021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Thiophene 10V, Negative-QTOFsplash10-001i-9000000000-39b4aa3e63c3ac07c2e42021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Thiophene 20V, Negative-QTOFsplash10-0a59-9000000000-c3bf730e742037db27022021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Thiophene 40V, Negative-QTOFsplash10-053r-9000000000-a93e605af8e97fbd6f072021-09-23Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum

IR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)2023-02-03FELIX labView Spectrum
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)2023-02-03FELIX labView Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
Biospecimen Locations
  • Feces
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected and Quantified0-11132.240 nmol/g wet fecesChildren (1-13 years old)Not Specified
Normal		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothNormal details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected and Quantified0-49401.791 nmol/g wet fecesChildren (1-13 years old)Not Specified
Treated celiac disease		 details
Associated Disorders and Diseases
Disease References
Celiac disease
  1. Di Cagno R, De Angelis M, De Pasquale I, Ndagijimana M, Vernocchi P, Ricciuti P, Gagliardi F, Laghi L, Crecchio C, Guerzoni ME, Gobbetti M, Francavilla R: Duodenal and faecal microbiota of celiac children: molecular, phenotype and metabolome characterization. BMC Microbiol. 2011 Oct 4;11:219. doi: 10.1186/1471-2180-11-219. [PubMed:21970810 ]
Associated OMIM IDs
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB000912
KNApSAcK IDC00041278
Chemspider ID7739
KEGG Compound IDC02595
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkThiophene
METLIN IDNot Available
PubChem Compound8030
PDB IDNot Available
ChEBI ID30856
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDMDB00029971
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. Wiles JA, Phadke AS, Bradbury BJ, Pucci MJ, Thanassi JA, Deshpande M: Selenophene-containing inhibitors of type IIA bacterial topoisomerases. J Med Chem. 2011 May 12;54(9):3418-25. doi: 10.1021/jm2002124. Epub 2011 Apr 13. [PubMed:21443219 ]
  2. Rodriguez-Arguelles MC, Mosquera-Vazquez S, Touron-Touceda P, Sanmartin-Matalobos J, Garcia-Deibe AM, Belicchi-Ferrari M, Pelosi G, Pelizzi C, Zani F: Complexes of 2-thiophenecarbonyl and isonicotinoyl hydrazones of 3-(N-methyl)isatin. A study of their antimicrobial activity. J Inorg Biochem. 2007 Jan;101(1):138-47. Epub 2006 Sep 19. [PubMed:17070919 ]
  3. Pillai AD, Rathod PD, Xavier FP, Vasu KK, Padh H, Sudarsanam V: Design, synthesis, and pharmacological evaluation of some 2-[4-morpholino]-3-aryl-5-substituted thiophenes as novel anti-inflammatory agents: generation of a novel anti-inflammatory pharmacophore. Bioorg Med Chem. 2004 Sep 1;12(17):4667-71. [PubMed:15358292 ]
  4. Nieves-Neira W, Rivera MI, Kohlhagen G, Hursey ML, Pourquier P, Sausville EA, Pommier Y: DNA protein cross-links produced by NSC 652287, a novel thiophene derivative active against human renal cancer cells. Mol Pharmacol. 1999 Sep;56(3):478-84. [PubMed:10462535 ]
  5. (). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .