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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
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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
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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
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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

$$$$
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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
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INCHI for HMDB0029718 (Thiophene)

InChI=1S/C4H4S/c1-2-4-5-3-1/h1-4H
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
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
Predicted Chromatographic Properties
Spectra
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)Not Available
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.. .