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Showing metabocard for 3-Thiophenemethanol (HMDB0041504)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-12 03:11:35 UTC
Update Date2023-02-21 17:28:47 UTC
HMDB IDHMDB0041504
Secondary Accession Numbers
  • HMDB41504
Metabolite Identification
Common Name3-Thiophenemethanol
Description3-Thiophenemethanol 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. Based on a literature review very few articles have been published on 3-Thiophenemethanol.
Structure
Data?1677000527
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0041504 (3-Thiophenemethanol)


  Mrv0541 05061312432D          

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

3D MOL for HMDB0041504 (3-Thiophenemethanol)

HMDB0041504
     RDKit          3D
3-Thiophenemethanol
 13 13  0  0  0  0  0  0  0  0999 V2000
   -1.8113   -1.2395   -0.2636 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4693    0.0958   -0.1227 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0386    0.2627   -0.0253 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9034   -0.7541   -0.0717 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2425   -0.4569    0.0285 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2361    1.2384    0.1841 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.5582    1.5244    0.1191 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6004   -1.4250    0.3042 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9162    0.5484    0.8059 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8656    0.7176   -0.9573 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5798   -1.8214   -0.1875 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0847   -1.1771    0.0081 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0194    2.4866    0.1783 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  1  0
  7  3  2  0
  1  8  1  0
  2  9  1  0
  2 10  1  0
  4 11  1  0
  5 12  1  0
  7 13  1  0
M  END
Download

3D SDF for HMDB0041504 (3-Thiophenemethanol)


  Mrv0541 05061312432D          

  7  7  0  0  0  0            999 V2000
   -0.0997    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    1.9393    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
    0.5678    1.1143    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
    0.9803   -0.1553    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  5  1  1  0  0  0  0
  5  3  1  0  0  0  0
  5  4  2  0  0  0  0
  6  3  1  0  0  0  0
  7  2  1  0  0  0  0
  7  4  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0041504

> <DATABASE_NAME>
hmdb

> <SMILES>
OCC1=CSC=C1

> <INCHI_IDENTIFIER>
InChI=1S/C5H6OS/c6-3-5-1-2-7-4-5/h1-2,4,6H,3H2

> <INCHI_KEY>
BOWIFWCBNWWZOG-UHFFFAOYSA-N

> <FORMULA>
C5H6OS

> <MOLECULAR_WEIGHT>
114.166

> <EXACT_MASS>
114.013935504

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_AVERAGE_POLARIZABILITY>
11.594677249421533

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
thiophen-3-ylmethanol

> <ALOGPS_LOGP>
0.91

> <JCHEM_LOGP>
0.9863380016666665

> <ALOGPS_LOGS>
-1.74

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.661509531958007

> <JCHEM_PKA_STRONGEST_BASIC>
-2.946855730721568

> <JCHEM_POLAR_SURFACE_AREA>
20.23

> <JCHEM_REFRACTIVITY>
29.9797

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.05e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
thiophen-3-ylmethanol

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0041504 (3-Thiophenemethanol)

HMDB0041504
     RDKit          3D
3-Thiophenemethanol
 13 13  0  0  0  0  0  0  0  0999 V2000
   -1.8113   -1.2395   -0.2636 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4693    0.0958   -0.1227 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0386    0.2627   -0.0253 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9034   -0.7541   -0.0717 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2425   -0.4569    0.0285 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2361    1.2384    0.1841 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.5582    1.5244    0.1191 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6004   -1.4250    0.3042 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9162    0.5484    0.8059 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8656    0.7176   -0.9573 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5798   -1.8214   -0.1875 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0847   -1.1771    0.0081 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0194    2.4866    0.1783 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  1  0
  7  3  2  0
  1  8  1  0
  2  9  1  0
  2 10  1  0
  4 11  1  0
  5 12  1  0
  7 13  1  0
M  END
Download

PDB for HMDB0041504 (3-Thiophenemethanol)

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      -0.186   1.175   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.290  -0.290   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.060   3.620   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       1.060   2.080   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -0.274   4.390   0.000  0.00  0.00           O+0
HETATM    7  S   UNK     0       1.830  -0.290   0.000  0.00  0.00           S+0
CONECT    1    2    5                                                       
CONECT    2    1    7                                                       
CONECT    3    5    6                                                       
CONECT    4    5    7                                                       
CONECT    5    1    3    4                                                  
CONECT    6    3                                                            
CONECT    7    2    4                                                       
MASTER        0    0    0    0    0    0    0    0    7    0   14    0
END
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3D PDB for HMDB0041504 (3-Thiophenemethanol)

COMPND    HMDB0041504
HETATM    1  O1  UNL     1      -1.811  -1.239  -0.264  1.00  0.00           O  
HETATM    2  C1  UNL     1      -1.469   0.096  -0.123  1.00  0.00           C  
HETATM    3  C2  UNL     1       0.039   0.263  -0.025  1.00  0.00           C  
HETATM    4  C3  UNL     1       0.903  -0.754  -0.072  1.00  0.00           C  
HETATM    5  C4  UNL     1       2.242  -0.457   0.029  1.00  0.00           C  
HETATM    6  S1  UNL     1       2.236   1.238   0.184  1.00  0.00           S  
HETATM    7  C5  UNL     1       0.558   1.524   0.119  1.00  0.00           C  
HETATM    8  H1  UNL     1      -2.600  -1.425   0.304  1.00  0.00           H  
HETATM    9  H2  UNL     1      -1.916   0.548   0.806  1.00  0.00           H  
HETATM   10  H3  UNL     1      -1.866   0.718  -0.957  1.00  0.00           H  
HETATM   11  H4  UNL     1       0.580  -1.821  -0.188  1.00  0.00           H  
HETATM   12  H5  UNL     1       3.085  -1.177   0.008  1.00  0.00           H  
HETATM   13  H6  UNL     1       0.019   2.487   0.178  1.00  0.00           H  
CONECT    1    2    8
CONECT    2    3    9   10
CONECT    3    4    7    7
CONECT    4    5    5   11
CONECT    5    6   12
CONECT    6    7
CONECT    7   13
END
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SMILES for HMDB0041504 (3-Thiophenemethanol)

OCC1=CSC=C1
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INCHI for HMDB0041504 (3-Thiophenemethanol)

InChI=1S/C5H6OS/c6-3-5-1-2-7-4-5/h1-2,4,6H,3H2
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
3-HydroxymethylthiopheneHMDB
3-ThienylmethanolHMDB
Thiophene-3-methanolHMDB
Chemical FormulaC5H6OS
Average Molecular Weight114.166
Monoisotopic Molecular Weight114.013935504
IUPAC Namethiophen-3-ylmethanol
Traditional Namethiophen-3-ylmethanol
CAS Registry Number71637-34-8
SMILES
OCC1=CSC=C1
InChI Identifier
InChI=1S/C5H6OS/c6-3-5-1-2-7-4-5/h1-2,4,6H,3H2
InChI KeyBOWIFWCBNWWZOG-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
  • Organic oxygen compound
  • Hydrocarbon derivative
  • Aromatic alcohol
  • Primary alcohol
  • Organooxygen compound
  • Alcohol
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
ProcessNot Available
Role
Biological role
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
Water Solubility2.05 g/LALOGPS
logP0.91ALOGPS
logP0.99ChemAxon
logS-1.7ALOGPS
pKa (Strongest Acidic)14.66ChemAxon
pKa (Strongest Basic)-2.9ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area20.23 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity29.98 m³·mol⁻¹ChemAxon
Polarizability11.59 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]+118.64131661259
DarkChem[M-H]-114.48731661259
DeepCCS[M+H]+122.95930932474
DeepCCS[M-H]-120.54330932474
DeepCCS[M-2H]-156.5930932474
DeepCCS[M+Na]+131.22530932474
AllCCS[M+H]+122.532859911
AllCCS[M+H-H2O]+117.732859911
AllCCS[M+NH4]+127.132859911
AllCCS[M+Na]+128.432859911
AllCCS[M-H]-123.732859911
AllCCS[M+Na-2H]-126.832859911
AllCCS[M+HCOO]-130.232859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
3-ThiophenemethanolOCC1=CSC=C11980.5Standard polar33892256
3-ThiophenemethanolOCC1=CSC=C11015.5Standard non polar33892256
3-ThiophenemethanolOCC1=CSC=C11011.3Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
3-Thiophenemethanol,1TMS,isomer #1C[Si](C)(C)OCC1=CSC=C11155.5Semi standard non polar33892256
3-Thiophenemethanol,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)OCC1=CSC=C11375.0Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 3-Thiophenemethanol GC-MS (Non-derivatized) - 70eV, Positivesplash10-01ot-9300000000-4c5f72fa4c81116459262017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Thiophenemethanol GC-MS (1 TMS) - 70eV, Positivesplash10-00dj-9300000000-9dec83d242ff547321c62017-10-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Thiophenemethanol 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 - 3-Thiophenemethanol 10V, Positive-QTOFsplash10-014j-8900000000-0f62cd5a506ca4bacdb32017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Thiophenemethanol 20V, Positive-QTOFsplash10-0002-9200000000-7690bf42418a917049322017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Thiophenemethanol 40V, Positive-QTOFsplash10-0002-9000000000-74f34d808a45b3159b132017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Thiophenemethanol 10V, Negative-QTOFsplash10-03di-1900000000-ba2d88f599c2a59d70c62017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Thiophenemethanol 20V, Negative-QTOFsplash10-03yi-9700000000-189db6826090b1323a772017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Thiophenemethanol 40V, Negative-QTOFsplash10-0a4i-9000000000-cb685c67ef06ef7a130a2017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Thiophenemethanol 10V, Negative-QTOFsplash10-01q9-9500000000-a400e3bb441f346ea1702021-09-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Thiophenemethanol 20V, Negative-QTOFsplash10-001i-9000000000-f238da7404e991031cad2021-09-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Thiophenemethanol 40V, Negative-QTOFsplash10-001i-9000000000-86a6ccaffbc10a67e9bd2021-09-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Thiophenemethanol 10V, Positive-QTOFsplash10-014j-9800000000-f1bf684480442fb8a8b12021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Thiophenemethanol 20V, Positive-QTOFsplash10-00kb-9200000000-19887a6c493c44ec07d82021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Thiophenemethanol 40V, Positive-QTOFsplash10-0udr-9000000000-c3081e0f3e1be42970212021-09-25Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum

IR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M-H]-)2023-02-04FELIX labView Spectrum
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)2023-02-04FELIX labView Spectrum
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)2023-02-04FELIX labView Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
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 IDFDB021476
KNApSAcK IDNot Available
Chemspider ID110164
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound123570
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
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.. .