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Showing metabocard for Thieno[2,3-b]pyridine (HMDB0258985)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 20:52:35 UTC
Update Date2021-09-26 23:16:15 UTC
HMDB IDHMDB0258985
Secondary Accession NumbersNone
Metabolite Identification
Common NameThieno[2,3-b]pyridine
Descriptionthieno[2,3-b]pyridine belongs to the class of organic compounds known as thienopyridines. These are heterocyclic compounds containing a thiophene ring fused to a pyridine ring. Thiophene is 5-membered ring consisting of four carbon atoms and one sulfur atom. Pyridine is a 6-membered ring consisting of five carbon atoms and one nitrogen center. Based on a literature review a significant number of articles have been published on thieno[2,3-b]pyridine. This compound has been identified in human blood as reported by (PMID: 31557052 ). Thieno[2,3-b]pyridine is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Thieno[2,3-b]pyridine 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 HMDB0258985 (Thieno[2,3-b]pyridine)


  Mrv1652309112122522D          

  9 10  0  0  0  0            999 V2000
    2.0701    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556    0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6411    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6411    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556    2.3479    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0701    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435    2.1904    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6284    1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435    0.8555    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  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
  5  6  2  0  0  0  0
  1  6  1  0  0  0  0
  4  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  3  9  1  0  0  0  0
M  END
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3D MOL for HMDB0258985 (Thieno[2,3-b]pyridine)

HMDB0258985
     RDKit          3D
Thieno[2,3-b]pyridine
 14 15  0  0  0  0  0  0  0  0999 V2000
   -1.9889   -0.1980   -0.2343 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0637    1.0295    0.3853 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8908    1.5838    0.7462 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.2860    0.9458    0.5005 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9162    1.3833    0.8327 S   0  0  0  0  0  0  0  0  0  0  0  0
    2.6900   -0.0093    0.1759 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6405   -0.7490   -0.2710 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4111   -0.2614   -0.1054 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8195   -0.8366   -0.4808 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9361   -0.6473   -0.5266 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0004    1.4913    0.5575 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7552   -0.2058    0.1475 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8759   -1.7226   -0.7507 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8756   -1.8036   -0.9767 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9  1  1  0
  8  4  1  0
  1 10  1  0
  2 11  1  0
  6 12  1  0
  7 13  1  0
  9 14  1  0
M  END
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3D SDF for HMDB0258985 (Thieno[2,3-b]pyridine)


  Mrv1652309112122522D          

  9 10  0  0  0  0            999 V2000
    2.0701    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556    0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6411    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6411    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556    2.3479    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0701    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435    2.1904    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6284    1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435    0.8555    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  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
  5  6  2  0  0  0  0
  1  6  1  0  0  0  0
  4  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  3  9  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0258985

> <DATABASE_NAME>
hmdb

> <SMILES>
S1C=CC2=C1N=CC=C2

> <INCHI_IDENTIFIER>
InChI=1S/C7H5NS/c1-2-6-3-5-9-7(6)8-4-1/h1-5H

> <INCHI_KEY>
SMZMHUCIDGHERP-UHFFFAOYSA-N

> <FORMULA>
C7H5NS

> <MOLECULAR_WEIGHT>
135.18

> <EXACT_MASS>
135.014270339

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
14

> <JCHEM_AVERAGE_POLARIZABILITY>
13.619530874899747

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
thieno[2,3-b]pyridine

> <ALOGPS_LOGP>
2.09

> <JCHEM_LOGP>
1.9990602403333333

> <ALOGPS_LOGS>
-2.06

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
2.519472914980615

> <JCHEM_POLAR_SURFACE_AREA>
12.89

> <JCHEM_REFRACTIVITY>
37.193799999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.18e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
thieno[2,3-b]pyridine

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0258985 (Thieno[2,3-b]pyridine)

HMDB0258985
     RDKit          3D
Thieno[2,3-b]pyridine
 14 15  0  0  0  0  0  0  0  0999 V2000
   -1.9889   -0.1980   -0.2343 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0637    1.0295    0.3853 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8908    1.5838    0.7462 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.2860    0.9458    0.5005 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9162    1.3833    0.8327 S   0  0  0  0  0  0  0  0  0  0  0  0
    2.6900   -0.0093    0.1759 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6405   -0.7490   -0.2710 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4111   -0.2614   -0.1054 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8195   -0.8366   -0.4808 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9361   -0.6473   -0.5266 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0004    1.4913    0.5575 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7552   -0.2058    0.1475 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8759   -1.7226   -0.7507 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8756   -1.8036   -0.9767 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9  1  1  0
  8  4  1  0
  1 10  1  0
  2 11  1  0
  6 12  1  0
  7 13  1  0
  9 14  1  0
M  END
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PDB for HMDB0258985 (Thieno[2,3-b]pyridine)

HEADER    PROTEIN                                 11-SEP-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-21         0                                  
HETATM    1  C   UNK     0       3.864   2.073   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.530   1.303   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.197   2.073   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.197   3.613   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0       2.530   4.383   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0       3.864   3.613   0.000  0.00  0.00           C+0
HETATM    7  S   UNK     0      -0.268   4.089   0.000  0.00  0.00           S+0
HETATM    8  C   UNK     0      -1.173   2.843   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -0.268   1.597   0.000  0.00  0.00           C+0
CONECT    1    2    6                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4    9                                                  
CONECT    4    3    5    7                                                  
CONECT    5    4    6                                                       
CONECT    6    5    1                                                       
CONECT    7    4    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8    3                                                       
MASTER        0    0    0    0    0    0    0    0    9    0   20    0
END
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3D PDB for HMDB0258985 (Thieno[2,3-b]pyridine)

COMPND    HMDB0258985
HETATM    1  C1  UNL     1      -1.989  -0.198  -0.234  1.00  0.00           C  
HETATM    2  C2  UNL     1      -2.064   1.029   0.385  1.00  0.00           C  
HETATM    3  N1  UNL     1      -0.891   1.584   0.746  1.00  0.00           N  
HETATM    4  C3  UNL     1       0.286   0.946   0.501  1.00  0.00           C  
HETATM    5  S1  UNL     1       1.916   1.383   0.833  1.00  0.00           S  
HETATM    6  C4  UNL     1       2.690  -0.009   0.176  1.00  0.00           C  
HETATM    7  C5  UNL     1       1.641  -0.749  -0.271  1.00  0.00           C  
HETATM    8  C6  UNL     1       0.411  -0.261  -0.105  1.00  0.00           C  
HETATM    9  C7  UNL     1      -0.820  -0.837  -0.481  1.00  0.00           C  
HETATM   10  H1  UNL     1      -2.936  -0.647  -0.527  1.00  0.00           H  
HETATM   11  H2  UNL     1      -3.000   1.491   0.557  1.00  0.00           H  
HETATM   12  H3  UNL     1       3.755  -0.206   0.147  1.00  0.00           H  
HETATM   13  H4  UNL     1       1.876  -1.723  -0.751  1.00  0.00           H  
HETATM   14  H5  UNL     1      -0.876  -1.804  -0.977  1.00  0.00           H  
CONECT    1    2    2    9   10
CONECT    2    3   11
CONECT    3    4    4
CONECT    4    5    8
CONECT    5    6
CONECT    6    7    7   12
CONECT    7    8   13
CONECT    8    9    9
CONECT    9   14
END
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SMILES for HMDB0258985 (Thieno[2,3-b]pyridine)

S1C=CC2=C1N=CC=C2
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INCHI for HMDB0258985 (Thieno[2,3-b]pyridine)

InChI=1S/C7H5NS/c1-2-6-3-5-9-7(6)8-4-1/h1-5H
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View in JSmolView Stereo Labels
Synonyms
ValueSource
Thieno(2,3-b)pyridineMeSH
Chemical FormulaC7H5NS
Average Molecular Weight135.18
Monoisotopic Molecular Weight135.014270339
IUPAC Namethieno[2,3-b]pyridine
Traditional Namethieno[2,3-b]pyridine
CAS Registry NumberNot Available
SMILES
S1C=CC2=C1N=CC=C2
InChI Identifier
InChI=1S/C7H5NS/c1-2-6-3-5-9-7(6)8-4-1/h1-5H
InChI KeySMZMHUCIDGHERP-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as thienopyridines. These are heterocyclic compounds containing a thiophene ring fused to a pyridine ring. Thiophene is 5-membered ring consisting of four carbon atoms and one sulfur atom. Pyridine is a 6-membered ring consisting of five carbon atoms and one nitrogen center.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassThienopyridines
Sub ClassNot Available
Direct ParentThienopyridines
Alternative Parents
Substituents
  • Thienopyridine
  • Pyridine
  • Heteroaromatic compound
  • Thiophene
  • Azacycle
  • Organic nitrogen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Organonitrogen compound
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological location
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
logP2.09ALOGPS
logP2ChemAxon
logS-2.1ALOGPS
pKa (Strongest Basic)2.52ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area12.89 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity37.19 m³·mol⁻¹ChemAxon
Polarizability13.62 ųChemAxon
Number of Rings2ChemAxon
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]+122.90830932474
DeepCCS[M-H]-120.33230932474
DeepCCS[M-2H]-156.72830932474
DeepCCS[M+Na]+131.53230932474
AllCCS[M+H]+124.132859911
AllCCS[M+H-H2O]+119.132859911
AllCCS[M+NH4]+128.832859911
AllCCS[M+Na]+130.132859911
AllCCS[M-H]-122.832859911
AllCCS[M+Na-2H]-124.232859911
AllCCS[M+HCOO]-125.932859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
Thieno[2,3-b]pyridineS1C=CC2=C1N=CC=C21871.3Standard polar33892256
Thieno[2,3-b]pyridineS1C=CC2=C1N=CC=C21183.4Standard non polar33892256
Thieno[2,3-b]pyridineS1C=CC2=C1N=CC=C21257.3Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Thieno[2,3-b]pyridine GC-MS (Non-derivatized) - 70eV, Positivesplash10-000i-1900000000-1f745bdb7b6c2978b8292021-09-24Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Thieno[2,3-b]pyridine GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView 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 ID255801
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
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. 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 ]