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Showing metabocard for Thiazolidine (HMDB0258978)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 20:52:02 UTC
Update Date2022-11-23 22:29:20 UTC
HMDB IDHMDB0258978
Secondary Accession NumbersNone
Metabolite Identification
Common NameThiazolidine
Descriptionthiazolidine belongs to the class of organic compounds known as thiazolidines. These are heterocyclic compounds containing a five-member saturated aliphatic ring with one nitrogen atom, one sulfur atom, three carbon atoms. Based on a literature review very few articles have been published on thiazolidine. This compound has been identified in human blood as reported by (PMID: 31557052 ). Thiazolidine is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Thiazolidine 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 HMDB0258978 (Thiazolidine)

10444
  Mrv0541 02241223112D          

  5  5  0  0  0  0            999 V2000
    1.9049    0.8905    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    2.3174   -0.3790    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.9848    0.1059    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7299    0.8905    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500    0.1059    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  4  1  0  0  0  0
  1  5  1  0  0  0  0
  2  3  1  0  0  0  0
  2  5  1  0  0  0  0
  3  4  1  0  0  0  0
M  END
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3D MOL for HMDB0258978 (Thiazolidine)

HMDB0258978
     RDKit          3D
THIAZOLIDINE
 12 12  0  0  0  0  0  0  0  0999 V2000
   -0.7051    0.5724    0.2000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1406   -0.8661    0.0736 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4832   -1.7016   -0.1258 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.4762   -0.1530   -0.1728 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4541    0.7556   -0.6360 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5741    0.9092    1.2341 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5167    1.1815   -0.2514 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8091   -1.0647   -0.7576 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5230   -1.2002    1.0663 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2635   -0.2170   -0.9314 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8283    0.0557    0.8400 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7634    1.7283   -0.5390 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  1  0
  5  1  1  0
  1  6  1  0
  1  7  1  0
  2  8  1  0
  2  9  1  0
  4 10  1  0
  4 11  1  0
  5 12  1  0
M  END
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3D SDF for HMDB0258978 (Thiazolidine)

10444
  Mrv0541 02241223112D          

  5  5  0  0  0  0            999 V2000
    1.9049    0.8905    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    2.3174   -0.3790    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.9848    0.1059    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7299    0.8905    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500    0.1059    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  4  1  0  0  0  0
  1  5  1  0  0  0  0
  2  3  1  0  0  0  0
  2  5  1  0  0  0  0
  3  4  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0258978

> <DATABASE_NAME>
hmdb

> <SMILES>
C1CSCN1

> <INCHI_IDENTIFIER>
InChI=1S/C3H7NS/c1-2-5-3-4-1/h4H,1-3H2

> <INCHI_KEY>
OGYGFUAIIOPWQD-UHFFFAOYSA-N

> <FORMULA>
C3H7NS

> <MOLECULAR_WEIGHT>
89.159

> <EXACT_MASS>
89.029919919

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_AVERAGE_POLARIZABILITY>
9.49288275094878

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1,3-thiazolidine

> <ALOGPS_LOGP>
-0.41

> <JCHEM_LOGP>
0.07332284233333337

> <ALOGPS_LOGS>
0.01

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_BASIC>
8.602295232751688

> <JCHEM_POLAR_SURFACE_AREA>
12.03

> <JCHEM_REFRACTIVITY>
24.994199999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
9.11e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
thiazolidine

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0258978 (Thiazolidine)

HMDB0258978
     RDKit          3D
THIAZOLIDINE
 12 12  0  0  0  0  0  0  0  0999 V2000
   -0.7051    0.5724    0.2000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1406   -0.8661    0.0736 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4832   -1.7016   -0.1258 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.4762   -0.1530   -0.1728 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4541    0.7556   -0.6360 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5741    0.9092    1.2341 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5167    1.1815   -0.2514 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8091   -1.0647   -0.7576 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5230   -1.2002    1.0663 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2635   -0.2170   -0.9314 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8283    0.0557    0.8400 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7634    1.7283   -0.5390 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  1  0
  5  1  1  0
  1  6  1  0
  1  7  1  0
  2  8  1  0
  2  9  1  0
  4 10  1  0
  4 11  1  0
  5 12  1  0
M  END
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PDB for HMDB0258978 (Thiazolidine)

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 10444                                             
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  S   UNK     0       3.556   1.662   0.000  0.00  0.00           S+0
HETATM    2  N   UNK     0       4.326  -0.707   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0       5.572   0.198   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.096   1.662   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.080   0.198   0.000  0.00  0.00           C+0
CONECT    1    4    5                                                       
CONECT    2    3    5                                                       
CONECT    3    2    4                                                       
CONECT    4    1    3                                                       
CONECT    5    1    2                                                       
MASTER        0    0    0    0    0    0    0    0    5    0   10    0
END
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3D PDB for HMDB0258978 (Thiazolidine)

COMPND    HMDB0258978
HETATM    1  C1  UNL     1      -0.705   0.572   0.200  1.00  0.00           C  
HETATM    2  C2  UNL     1      -1.141  -0.866   0.074  1.00  0.00           C  
HETATM    3  S1  UNL     1       0.483  -1.702  -0.126  1.00  0.00           S  
HETATM    4  C3  UNL     1       1.476  -0.153  -0.173  1.00  0.00           C  
HETATM    5  N1  UNL     1       0.454   0.756  -0.636  1.00  0.00           N  
HETATM    6  H1  UNL     1      -0.574   0.909   1.234  1.00  0.00           H  
HETATM    7  H2  UNL     1      -1.517   1.182  -0.251  1.00  0.00           H  
HETATM    8  H3  UNL     1      -1.809  -1.065  -0.758  1.00  0.00           H  
HETATM    9  H4  UNL     1      -1.523  -1.200   1.066  1.00  0.00           H  
HETATM   10  H5  UNL     1       2.263  -0.217  -0.931  1.00  0.00           H  
HETATM   11  H6  UNL     1       1.828   0.056   0.840  1.00  0.00           H  
HETATM   12  H7  UNL     1       0.763   1.728  -0.539  1.00  0.00           H  
CONECT    1    2    5    6    7
CONECT    2    3    8    9
CONECT    3    4
CONECT    4    5   10   11
CONECT    5   12
END
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SMILES for HMDB0258978 (Thiazolidine)

C1CSCN1
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INCHI for HMDB0258978 (Thiazolidine)

InChI=1S/C3H7NS/c1-2-5-3-4-1/h4H,1-3H2
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View in JSmolView Stereo Labels
Synonyms
ValueSource
1-Thia-3-azacyclopentaneChEBI
TetrahydrothiazoleChEBI
Chemical FormulaC3H7NS
Average Molecular Weight89.159
Monoisotopic Molecular Weight89.029919919
IUPAC Name1,3-thiazolidine
Traditional Namethiazolidine
CAS Registry NumberNot Available
SMILES
C1CSCN1
InChI Identifier
InChI=1S/C3H7NS/c1-2-5-3-4-1/h4H,1-3H2
InChI KeyOGYGFUAIIOPWQD-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as thiazolidines. These are heterocyclic compounds containing a five-member saturated aliphatic ring with one nitrogen atom, one sulfur atom, three carbon atoms.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassAzolidines
Sub ClassThiazolidines
Direct ParentThiazolidines
Alternative Parents
Substituents
  • Thiazolidine
  • Azacycle
  • Dialkylthioether
  • Hemithioaminal
  • Thioether
  • Secondary amine
  • Secondary aliphatic amine
  • Organic nitrogen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Organonitrogen compound
  • Amine
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic 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
Predicted Chromatographic Properties
Spectra
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 IDC00000308
Chemspider ID10013
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkThiazolidine
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI ID50120
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1288931
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 ]

Enzymes

Enzyme Details
1. Abasic site processing protein HMCES
General function:
Not Available
Specific function:
Sensor of abasic sites in single-stranded DNA (ssDNA) required to preserve genome integrity by promoting error-free repair of abasic sites (PubMed:30554877, PubMed:31235915, PubMed:31235913). Acts as an enzyme that recognizes and binds abasic sites in ssDNA at replication forks and chemically modifies the lesion by forming a covalent cross-link with DNA: forms a stable thiazolidine linkage between a ring-opened abasic site and the alpha-amino and sulfhydryl substituents of its N-terminal catalytic cysteine residue (PubMed:30554877, PubMed:31235913). The HMCES DNA-protein cross-link is then degraded by the proteasome (PubMed:30554877). Promotes error-free repair of abasic sites by acting as a 'suicide' enzyme that is degraded, thereby protecting abasic sites from translesion synthesis (TLS) polymerases and endonucleases that are error-prone and would generate mutations and double-strand breaks (PubMed:30554877). Has preference for ssDNA, but can also accommodate double-stranded DNA with 3' or 5' overhang (dsDNA), and dsDNA-ssDNA 3' junction (PubMed:31235915, PubMed:31806351). Also involved in class switch recombination (CSR) in B-cells independently of the formation of a DNA-protein cross-link: acts by binding and protecting ssDNA overhangs to promote DNA double-strand break repair through the microhomology-mediated alternative-end-joining (Alt-EJ) pathway (By similarity). Acts as a protease: mediates autocatalytic processing of its N-terminal methionine in order to expose the catalytic cysteine (By similarity).
Gene Name:
HMCES
Uniprot ID:
Q96FZ2
Molecular weight:
40574.585