Hmdb loader

Showing metabocard for Thiophen-3-carboxyaldehyde (HMDB0302373)

Jump To Section:
IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesXML
Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2021-09-23 17:17:42 UTC
Update Date2021-09-23 17:17:42 UTC
HMDB IDHMDB0302373
Secondary Accession NumbersNone
Metabolite Identification
Common NameThiophen-3-carboxyaldehyde
DescriptionThiophen-3-carboxyaldehyde is a member of the class of compounds known as aryl-aldehydes. Aryl-aldehydes are compounds containing an aldehyde group directly attached to an aromatic ring. Thiophen-3-carboxyaldehyde is slightly soluble (in water) and an extremely weak basic (essentially neutral) compound (based on its pKa). Thiophen-3-carboxyaldehyde can be found in kohlrabi, which makes thiophen-3-carboxyaldehyde a potential biomarker for the consumption of this food product.
Structure
Thumb
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0302373 (Thiophen-3-carboxyaldehyde)


  Mrv1533007301516532D          

  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  2  0  0  0  0
  7  2  1  0  0  0  0
  7  4  1  0  0  0  0
M  END
Download

3D MOL for HMDB0302373 (Thiophen-3-carboxyaldehyde)

HMDB0302373
     RDKit          3D
Thiophen-3-carboxyaldehyde
 11 11  0  0  0  0  0  0  0  0999 V2000
   -1.9321   -1.7122    0.0855 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7500   -0.5151   -0.1459 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3724    0.0353   -0.0623 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7060   -0.6899    0.2524 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9139   -0.0502    0.2918 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5089    1.5546   -0.1136 S   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1710    1.3711   -0.3207 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5931    0.1003   -0.4024 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6916   -1.7740    0.4840 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9066   -0.4657    0.5272 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9083    2.1457   -0.5960 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  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
  2  8  1  0
  4  9  1  0
  5 10  1  0
  7 11  1  0
M  END
Download

3D SDF for HMDB0302373 (Thiophen-3-carboxyaldehyde)


  Mrv1533007301516532D          

  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  2  0  0  0  0
  7  2  1  0  0  0  0
  7  4  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0302373

> <DATABASE_NAME>
hmdb

> <SMILES>
O=CC1=CSC=C1

> <INCHI_IDENTIFIER>
InChI=1S/C5H4OS/c6-3-5-1-2-7-4-5/h1-4H

> <INCHI_KEY>
RBIGKSZIQCTIJF-UHFFFAOYSA-N

> <FORMULA>
C5H4OS

> <MOLECULAR_WEIGHT>
112.15

> <EXACT_MASS>
111.998285923

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
11

> <JCHEM_AVERAGE_POLARIZABILITY>
10.70066895114245

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
thiophene-3-carbaldehyde

> <ALOGPS_LOGP>
1.05

> <JCHEM_LOGP>
1.4661901136666664

> <ALOGPS_LOGS>
-1.96

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-7.182863282677923

> <JCHEM_POLAR_SURFACE_AREA>
17.07

> <JCHEM_REFRACTIVITY>
29.747800000000005

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.22e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-thiophenecarboxaldehyde

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0302373 (Thiophen-3-carboxyaldehyde)

HMDB0302373
     RDKit          3D
Thiophen-3-carboxyaldehyde
 11 11  0  0  0  0  0  0  0  0999 V2000
   -1.9321   -1.7122    0.0855 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7500   -0.5151   -0.1459 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3724    0.0353   -0.0623 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7060   -0.6899    0.2524 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9139   -0.0502    0.2918 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5089    1.5546   -0.1136 S   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1710    1.3711   -0.3207 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5931    0.1003   -0.4024 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6916   -1.7740    0.4840 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9066   -0.4657    0.5272 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9083    2.1457   -0.5960 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  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
  2  8  1  0
  4  9  1  0
  5 10  1  0
  7 11  1  0
M  END
Download

PDB for HMDB0302373 (Thiophen-3-carboxyaldehyde)

HEADER    PROTEIN                                 30-JUL-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   30-JUL-15         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
Download

3D PDB for HMDB0302373 (Thiophen-3-carboxyaldehyde)

COMPND    HMDB0302373
HETATM    1  O1  UNL     1      -1.932  -1.712   0.085  1.00  0.00           O  
HETATM    2  C1  UNL     1      -1.750  -0.515  -0.146  1.00  0.00           C  
HETATM    3  C2  UNL     1      -0.372   0.035  -0.062  1.00  0.00           C  
HETATM    4  C3  UNL     1       0.706  -0.690   0.252  1.00  0.00           C  
HETATM    5  C4  UNL     1       1.914  -0.050   0.292  1.00  0.00           C  
HETATM    6  S1  UNL     1       1.509   1.555  -0.114  1.00  0.00           S  
HETATM    7  C5  UNL     1      -0.171   1.371  -0.321  1.00  0.00           C  
HETATM    8  H1  UNL     1      -2.593   0.100  -0.402  1.00  0.00           H  
HETATM    9  H2  UNL     1       0.692  -1.774   0.484  1.00  0.00           H  
HETATM   10  H3  UNL     1       2.907  -0.466   0.527  1.00  0.00           H  
HETATM   11  H4  UNL     1      -0.908   2.146  -0.596  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    8
CONECT    3    4    7    7
CONECT    4    5    5    9
CONECT    5    6   10
CONECT    6    7
CONECT    7   11
END
Download

SMILES for HMDB0302373 (Thiophen-3-carboxyaldehyde)

O=CC1=CSC=C1
Download

INCHI for HMDB0302373 (Thiophen-3-carboxyaldehyde)

InChI=1S/C5H4OS/c6-3-5-1-2-7-4-5/h1-4H
Download
View in JSmolView Stereo Labels
Synonyms
ValueSource
3-ThiophenecarboxaldehydeChEBI
Chemical FormulaC5H4OS
Average Molecular Weight112.15
Monoisotopic Molecular Weight111.998285923
IUPAC Namethiophene-3-carbaldehyde
Traditional Name3-thiophenecarboxaldehyde
CAS Registry NumberNot Available
SMILES
O=CC1=CSC=C1
InChI Identifier
InChI=1S/C5H4OS/c6-3-5-1-2-7-4-5/h1-4H
InChI KeyRBIGKSZIQCTIJF-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as aryl-aldehydes. Aryl-aldehydes are compounds containing an aldehyde group directly attached to an aromatic ring.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbonyl compounds
Direct ParentAryl-aldehydes
Alternative Parents
Substituents
  • Aryl-aldehyde
  • Heteroaromatic compound
  • Thiophene
  • Organoheterocyclic compound
  • Organic oxide
  • Hydrocarbon derivative
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Source
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
logP1.05ALOGPS
logP1.47ChemAxon
logS-2ALOGPS
pKa (Strongest Basic)-7.2ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area17.07 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity29.75 m³·mol⁻¹ChemAxon
Polarizability10.7 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
AllCCS[M+H]+121.65532859911
AllCCS[M+H-H2O]+116.74632859911
AllCCS[M+Na]+127.56432859911
AllCCS[M+NH4]+126.2432859911
AllCCS[M-H]-121.10532859911
AllCCS[M+Na-2H]-124.12332859911
AllCCS[M+HCOO]-127.46332859911
DeepCCS[M+H]+121.67530932474
DeepCCS[M-H]-119.28130932474
DeepCCS[M-2H]-155.30630932474
DeepCCS[M+Na]+130.07130932474

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Predicted by Siyang on May 30, 202213.4101 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20221.74 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid1471.7 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid532.8 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid213.3 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid382.3 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid190.0 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid409.7 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 Acid557.7 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)339.8 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid963.6 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid322.8 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid983.1 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid370.9 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid395.2 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate659.7 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA503.7 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water157.5 seconds40023050

Predicted Kovats Retention Indices

Not Available
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Thiophen-3-carboxyaldehyde 10V, Positive-QTOFsplash10-03di-0900000000-e419954f748a05010d962016-08-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Thiophen-3-carboxyaldehyde 20V, Positive-QTOFsplash10-03di-1900000000-b1dae361abb6ce3c78012016-08-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Thiophen-3-carboxyaldehyde 40V, Positive-QTOFsplash10-03xr-8900000000-b8bddcf1bb71afa762562016-08-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Thiophen-3-carboxyaldehyde 10V, Negative-QTOFsplash10-03di-0900000000-ed0197387ada7820435d2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Thiophen-3-carboxyaldehyde 20V, Negative-QTOFsplash10-03di-1900000000-90c021808594f76131a72016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Thiophen-3-carboxyaldehyde 40V, Negative-QTOFsplash10-0a4i-9000000000-8f6d60101c55011c9fe32016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Thiophen-3-carboxyaldehyde 10V, Positive-QTOFsplash10-01p9-9600000000-b6660df7a3dcc39e440d2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Thiophen-3-carboxyaldehyde 20V, Positive-QTOFsplash10-029l-9300000000-bcb7566d60f6a1bd65d32021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Thiophen-3-carboxyaldehyde 40V, Positive-QTOFsplash10-000l-9000000000-3da812516148acc64e532021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Thiophen-3-carboxyaldehyde 10V, Negative-QTOFsplash10-001i-9100000000-57f0b556557fb052dff52021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Thiophen-3-carboxyaldehyde 20V, Negative-QTOFsplash10-001i-9000000000-7d99ce9954aa98dbedf62021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Thiophen-3-carboxyaldehyde 40V, Negative-QTOFsplash10-001i-9000000000-cf7e9d5b38c86beb946a2021-10-21Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
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 IDFDB004321
KNApSAcK IDNot Available
Chemspider ID61443
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound68135
PDB IDNot Available
ChEBI ID87611
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1193341
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available