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Showing metabocard for Thiophene-2-carboxylic acid (HMDB0259027)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 20:55:56 UTC
Update Date2022-11-23 22:29:20 UTC
HMDB IDHMDB0259027
Secondary Accession NumbersNone
Metabolite Identification
Common NameThiophene-2-carboxylic acid
Descriptionthiophene-2-carboxylic acid, also known as 2-thiophenecarboxylate or 2-carboxythiophene, belongs to the class of organic compounds known as thiophene carboxylic acids. Thiophene carboxylic acids are compounds containing a thiophene ring which bears a carboxylic acid group. Based on a literature review very few articles have been published on thiophene-2-carboxylic acid. This compound has been identified in human blood as reported by (PMID: 31557052 ). Thiophene-2-carboxylic acid is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Thiophene-2-carboxylic acid is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0259027 (Thiophene-2-carboxylic acid)


  Mrv0541 05041401212D          

  8  8  0  0  0  0            999 V2000
    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
    0.5678    1.9393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1467    2.3518    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2822    2.3518    0.0000 O   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
  2  1  1  0  0  0  0
  3  1  2  0  0  0  0
  4  2  2  0  0  0  0
  5  4  1  0  0  0  0
  6  5  1  0  0  0  0
  7  5  2  0  0  0  0
  8  3  1  0  0  0  0
  8  4  1  0  0  0  0
M  END
Download

3D MOL for HMDB0259027 (Thiophene-2-carboxylic acid)

HMDB0259027
     RDKit          3D
THIOPHENE-2-CARBOXYLIC ACID
 12 12  0  0  0  0  0  0  0  0999 V2000
   -2.2388    1.4642    0.2520 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8967    0.2593    0.2850 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7913   -0.7730    0.4584 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4461   -0.0135    0.1248 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5627    0.8838   -0.0541 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8152    0.3969   -0.1768 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9641   -0.9601   -0.1107 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3721   -1.5125    0.1180 S   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3180   -1.2044   -0.2849 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3568    1.9799   -0.0970 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7249    1.0264   -0.3270 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8952   -1.5470   -0.1879 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  4  1  0
  3  9  1  0
  5 10  1  0
  6 11  1  0
  7 12  1  0
M  END
Download

3D SDF for HMDB0259027 (Thiophene-2-carboxylic acid)


  Mrv0541 05041401212D          

  8  8  0  0  0  0            999 V2000
    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
    0.5678    1.9393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1467    2.3518    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2822    2.3518    0.0000 O   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
  2  1  1  0  0  0  0
  3  1  2  0  0  0  0
  4  2  2  0  0  0  0
  5  4  1  0  0  0  0
  6  5  1  0  0  0  0
  7  5  2  0  0  0  0
  8  3  1  0  0  0  0
  8  4  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0259027

> <DATABASE_NAME>
hmdb

> <SMILES>
OC(=O)C1=CC=CS1

> <INCHI_IDENTIFIER>
InChI=1S/C5H4O2S/c6-5(7)4-2-1-3-8-4/h1-3H,(H,6,7)

> <INCHI_KEY>
QERYCTSHXKAMIS-UHFFFAOYSA-N

> <FORMULA>
C5H4O2S

> <MOLECULAR_WEIGHT>
128.149

> <EXACT_MASS>
127.993200062

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_AVERAGE_POLARIZABILITY>
11.627639645626306

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
thiophene-2-carboxylic acid

> <ALOGPS_LOGP>
1.43

> <JCHEM_LOGP>
1.543710097

> <ALOGPS_LOGS>
-1.83

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.3420605132553685

> <JCHEM_PKA_STRONGEST_BASIC>
-9.72594967075757

> <JCHEM_POLAR_SURFACE_AREA>
37.3

> <JCHEM_REFRACTIVITY>
30.204100000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.89e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
thiophene-2-carboxylic acid

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0259027 (Thiophene-2-carboxylic acid)

HMDB0259027
     RDKit          3D
THIOPHENE-2-CARBOXYLIC ACID
 12 12  0  0  0  0  0  0  0  0999 V2000
   -2.2388    1.4642    0.2520 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8967    0.2593    0.2850 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7913   -0.7730    0.4584 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4461   -0.0135    0.1248 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5627    0.8838   -0.0541 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8152    0.3969   -0.1768 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9641   -0.9601   -0.1107 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3721   -1.5125    0.1180 S   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3180   -1.2044   -0.2849 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3568    1.9799   -0.0970 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7249    1.0264   -0.3270 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8952   -1.5470   -0.1879 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  4  1  0
  3  9  1  0
  5 10  1  0
  6 11  1  0
  7 12  1  0
M  END
Download

PDB for HMDB0259027 (Thiophene-2-carboxylic acid)

HEADER    PROTEIN                                 04-MAY-14   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-MAY-14         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.000   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  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    8  S   UNK     0       0.000   0.000   0.000  0.00  0.00           S+0
CONECT    1    2    3                                                       
CONECT    2    1    4                                                       
CONECT    3    1    8                                                       
CONECT    4    2    5    8                                                  
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5                                                            
CONECT    8    3    4                                                       
MASTER        0    0    0    0    0    0    0    0    8    0   16    0
END
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3D PDB for HMDB0259027 (Thiophene-2-carboxylic acid)

COMPND    HMDB0259027
HETATM    1  O1  UNL     1      -2.239   1.464   0.252  1.00  0.00           O  
HETATM    2  C1  UNL     1      -1.897   0.259   0.285  1.00  0.00           C  
HETATM    3  O2  UNL     1      -2.791  -0.773   0.458  1.00  0.00           O  
HETATM    4  C2  UNL     1      -0.446  -0.014   0.125  1.00  0.00           C  
HETATM    5  C3  UNL     1       0.563   0.884  -0.054  1.00  0.00           C  
HETATM    6  C4  UNL     1       1.815   0.397  -0.177  1.00  0.00           C  
HETATM    7  C5  UNL     1       1.964  -0.960  -0.111  1.00  0.00           C  
HETATM    8  S1  UNL     1       0.372  -1.513   0.118  1.00  0.00           S  
HETATM    9  H1  UNL     1      -3.318  -1.204  -0.285  1.00  0.00           H  
HETATM   10  H2  UNL     1       0.357   1.980  -0.097  1.00  0.00           H  
HETATM   11  H3  UNL     1       2.725   1.026  -0.327  1.00  0.00           H  
HETATM   12  H4  UNL     1       2.895  -1.547  -0.188  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3    9
CONECT    4    5    5    8
CONECT    5    6   10
CONECT    6    7    7   11
CONECT    7    8   12
END
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SMILES for HMDB0259027 (Thiophene-2-carboxylic acid)

OC(=O)C1=CC=CS1
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INCHI for HMDB0259027 (Thiophene-2-carboxylic acid)

InChI=1S/C5H4O2S/c6-5(7)4-2-1-3-8-4/h1-3H,(H,6,7)
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View in JSmolView Stereo Labels
Synonyms
ValueSource
2-CarboxythiopheneChEBI
2-Thenoic acidChEBI
2-Thiophenecarboxylic acidChEBI
2-Thiophenic acidChEBI
alpha-Thiophenecarboxylic acidChEBI
Tenoic acidChEBI
Thiophene-2-carbixylic acidKegg
RhinotrophylKegg
2-ThenoateGenerator
2-ThiophenecarboxylateGenerator
2-ThiophenateGenerator
a-ThiophenecarboxylateGenerator
a-Thiophenecarboxylic acidGenerator
alpha-ThiophenecarboxylateGenerator
Α-thiophenecarboxylateGenerator
Α-thiophenecarboxylic acidGenerator
TenoateGenerator
Thiophene-2-carbixylateGenerator
Thiophene-2-carboxylateGenerator
Thiophene-2-carboxylate, sodium saltMeSH
Sodium thiophenecarboxylateMeSH
Thiophene-2-carboxylate, 2-(14)C-labeledMeSH
2-Thiophencarboxylic acidMeSH
2-Thiophene carboxylic acidMeSH
Chemical FormulaC5H4O2S
Average Molecular Weight128.149
Monoisotopic Molecular Weight127.993200062
IUPAC Namethiophene-2-carboxylic acid
Traditional Namethiophene-2-carboxylic acid
CAS Registry NumberNot Available
SMILES
OC(=O)C1=CC=CS1
InChI Identifier
InChI=1S/C5H4O2S/c6-5(7)4-2-1-3-8-4/h1-3H,(H,6,7)
InChI KeyQERYCTSHXKAMIS-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as thiophene carboxylic acids. Thiophene carboxylic acids are compounds containing a thiophene ring which bears a carboxylic acid group.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassThiophenes
Sub ClassThiophene carboxylic acids and derivatives
Direct ParentThiophene carboxylic acids
Alternative Parents
Substituents
  • Thiophene carboxylic acid
  • Heteroaromatic compound
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Carboxylic acid derivative
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
logP1.43ALOGPS
logP1.54ChemAxon
logS-1.8ALOGPS
pKa (Strongest Acidic)3.34ChemAxon
pKa (Strongest Basic)-9.7ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area37.3 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity30.2 m³·mol⁻¹ChemAxon
Polarizability11.63 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
DeepCCS[M+H]+127.36730932474
DeepCCS[M-H]-125.28430932474
DeepCCS[M-2H]-160.8730932474
DeepCCS[M+Na]+135.22130932474
AllCCS[M+H]+128.132859911
AllCCS[M+H-H2O]+123.632859911
AllCCS[M+NH4]+132.332859911
AllCCS[M+Na]+133.532859911
AllCCS[M-H]-120.432859911
AllCCS[M+Na-2H]-123.032859911
AllCCS[M+HCOO]-126.032859911

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. Predicted by Afia on May 17, 2022.3.67 minutes32390414
Predicted by Siyang on May 30, 202210.706 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20222.35 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid1190.3 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid411.5 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid141.3 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid284.7 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid175.5 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid330.5 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 Acid398.9 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)423.1 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid831.5 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid283.9 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid947.1 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid280.5 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid330.2 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate559.0 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA349.8 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water166.8 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
THIOPHENE-2-CARBOXYLIC ACIDOC(=O)C1=CC=CS12583.5Standard polar33892256
THIOPHENE-2-CARBOXYLIC ACIDOC(=O)C1=CC=CS11179.1Standard non polar33892256
THIOPHENE-2-CARBOXYLIC ACIDOC(=O)C1=CC=CS11252.4Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Thiophene-2-carboxylic acid GC-MS (Non-derivatized) - 70eV, Positivesplash10-056r-9600000000-707a77364f3ef026827a2021-09-24Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Thiophene-2-carboxylic acid GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Thiophene-2-carboxylic acid GC-MS (TMS_1_1) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Thiophene-2-carboxylic acid GC-MS (TBDMS_1_1) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Experimental LC-MS/MSLC-MS/MS Spectrum - Thiophene-2-carboxylic acid 20V, Positive-QTOFsplash10-01p9-9600000000-b1e993e9c8a19038b0382021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Thiophene-2-carboxylic acid 10V, Positive-QTOFsplash10-004r-4900000000-8671ea6748b8091aa3572021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Thiophene-2-carboxylic acid 30V, Positive-QTOFsplash10-03dr-6900000000-3e7eda432f0a5200cc762021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Thiophene-2-carboxylic acid 40V, Positive-QTOFsplash10-03dr-6900000000-82add2315699ae49effd2021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Thiophene-2-carboxylic acid 20V, Positive-QTOFsplash10-01p9-9600000000-9fde5628ca565ea279992021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Thiophene-2-carboxylic acid 10V, Positive-QTOFsplash10-004r-4900000000-dd6aa708023217423e7b2021-09-20HMDB team, MONAView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID10250
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI ID71241
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1181031
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]