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Showing metabocard for Rhodanine (HMDB0257201)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 17:57:03 UTC
Update Date2022-11-23 22:29:19 UTC
HMDB IDHMDB0257201
Secondary Accession NumbersNone
Metabolite Identification
Common NameRhodanine
Description4-hydroxy-2,5-dihydro-1,3-thiazole-2-thione, also known as 2-thioxo-4-thiazolidinone, belongs to the class of organic compounds known as thiazolidinethiones. These are heterocyclic compounds containing a thiazolidinethione ring which bears one thioketone group. Based on a literature review very few articles have been published on 4-hydroxy-2,5-dihydro-1,3-thiazole-2-thione. This compound has been identified in human blood as reported by (PMID: 31557052 ). Rhodanine is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Rhodanine 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 HMDB0257201 (Rhodanine)


  Mrv1652309112119572D          

  7  7  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
    0.1553   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3297   -0.8227    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 N   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 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  5  7  1  0  0  0  0
  1  7  1  0  0  0  0
M  END
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3D MOL for HMDB0257201 (Rhodanine)

HMDB0257201
     RDKit          3D
RHODANINE
 10 10  0  0  0  0  0  0  0  0999 V2000
   -1.3366   -1.6778   -0.6172 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6330   -0.7184   -0.1444 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2242    0.6204    0.0780 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2546    1.6731   -0.2062 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.4762    0.3451   -0.0716 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0858    0.5383   -0.2387 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.7113   -0.8227    0.1994 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5678    0.8003    1.0934 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9421    0.9031   -0.7157 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1757   -1.6612    0.6230 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  1  0
  5  6  2  0
  5  7  1  0
  7  2  1  0
  3  8  1  0
  3  9  1  0
  7 10  1  0
M  END
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3D SDF for HMDB0257201 (Rhodanine)


  Mrv1652309112119572D          

  7  7  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
    0.1553   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3297   -0.8227    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 N   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 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  5  7  1  0  0  0  0
  1  7  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0257201

> <DATABASE_NAME>
hmdb

> <SMILES>
O=C1CSC(=S)N1

> <INCHI_IDENTIFIER>
InChI=1S/C3H3NOS2/c5-2-1-7-3(6)4-2/h1H2,(H,4,5,6)

> <INCHI_KEY>
KIWUVOGUEXMXSV-UHFFFAOYSA-N

> <FORMULA>
C3H3NOS2

> <MOLECULAR_WEIGHT>
133.18

> <EXACT_MASS>
132.965606069

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
10

> <JCHEM_AVERAGE_POLARIZABILITY>
11.902193542799553

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-sulfanylidene-1,3-thiazolidin-4-one

> <ALOGPS_LOGP>
0.24

> <JCHEM_LOGP>
0.6121053346666666

> <ALOGPS_LOGS>
-2.03

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.216512453522629

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.344811070185253

> <JCHEM_PKA_STRONGEST_BASIC>
-8.92303988590881

> <JCHEM_POLAR_SURFACE_AREA>
29.1

> <JCHEM_REFRACTIVITY>
33.5305

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.26e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
rhodanine

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0257201 (Rhodanine)

HMDB0257201
     RDKit          3D
RHODANINE
 10 10  0  0  0  0  0  0  0  0999 V2000
   -1.3366   -1.6778   -0.6172 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6330   -0.7184   -0.1444 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2242    0.6204    0.0780 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2546    1.6731   -0.2062 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.4762    0.3451   -0.0716 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0858    0.5383   -0.2387 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.7113   -0.8227    0.1994 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5678    0.8003    1.0934 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9421    0.9031   -0.7157 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1757   -1.6612    0.6230 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  1  0
  5  6  2  0
  5  7  1  0
  7  2  1  0
  3  8  1  0
  3  9  1  0
  7 10  1  0
M  END
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PDB for HMDB0257201 (Rhodanine)

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       1.830  -0.290   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  O   UNK     0      -0.615  -1.536   0.000  0.00  0.00           O+0
HETATM    4  N   UNK     0      -0.186   1.175   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0       1.060   2.080   0.000  0.00  0.00           C+0
HETATM    6  S   UNK     0       1.060   3.620   0.000  0.00  0.00           S+0
HETATM    7  S   UNK     0       2.306   1.175   0.000  0.00  0.00           S+0
CONECT    1    2    7                                                       
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    1                                                       
MASTER        0    0    0    0    0    0    0    0    7    0   14    0
END
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3D PDB for HMDB0257201 (Rhodanine)

COMPND    HMDB0257201
HETATM    1  O1  UNL     1      -1.337  -1.678  -0.617  1.00  0.00           O  
HETATM    2  C1  UNL     1      -0.633  -0.718  -0.144  1.00  0.00           C  
HETATM    3  C2  UNL     1      -1.224   0.620   0.078  1.00  0.00           C  
HETATM    4  S1  UNL     1       0.255   1.673  -0.206  1.00  0.00           S  
HETATM    5  C3  UNL     1       1.476   0.345  -0.072  1.00  0.00           C  
HETATM    6  S2  UNL     1       3.086   0.538  -0.239  1.00  0.00           S  
HETATM    7  N1  UNL     1       0.711  -0.823   0.199  1.00  0.00           N  
HETATM    8  H1  UNL     1      -1.568   0.800   1.093  1.00  0.00           H  
HETATM    9  H2  UNL     1      -1.942   0.903  -0.716  1.00  0.00           H  
HETATM   10  H3  UNL     1       1.176  -1.661   0.623  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    7
CONECT    3    4    8    9
CONECT    4    5
CONECT    5    6    6    7
CONECT    7   10
END
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SMILES for HMDB0257201 (Rhodanine)

O=C1CSC(=S)N1
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INCHI for HMDB0257201 (Rhodanine)

InChI=1S/C3H3NOS2/c5-2-1-7-3(6)4-2/h1H2,(H,4,5,6)
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View in JSmolView Stereo Labels
Synonyms
ValueSource
2-Thioxo-4-thiazolidinoneKegg
Chemical FormulaC3H3NOS2
Average Molecular Weight133.18
Monoisotopic Molecular Weight132.965606069
IUPAC Name2-sulfanylidene-1,3-thiazolidin-4-one
Traditional Namerhodanine
CAS Registry NumberNot Available
SMILES
O=C1CSC(=S)N1
InChI Identifier
InChI=1S/C3H3NOS2/c5-2-1-7-3(6)4-2/h1H2,(H,4,5,6)
InChI KeyKIWUVOGUEXMXSV-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as thiazolidinethiones. These are heterocyclic compounds containing a thiazolidinethione ring which bears one thioketone group.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassAzolidines
Sub ClassThiazolidines
Direct ParentThiazolidinethiones
Alternative Parents
Substituents
  • Thiazolidinethione
  • Cyclic dithiocarbamic acid ester
  • Dithiocarbamic acid ester
  • Azacycle
  • Carboxylic acid derivative
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organosulfur compound
  • Organooxygen compound
  • Organonitrogen compound
  • Carbonyl group
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
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
logP0.24ALOGPS
logP0.61ChemAxon
logS-2ALOGPS
pKa (Strongest Acidic)9.34ChemAxon
pKa (Strongest Basic)-8.9ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area29.1 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity33.53 m³·mol⁻¹ChemAxon
Polarizability11.9 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]+130.88530932474
DeepCCS[M-H]-128.96430932474
DeepCCS[M-2H]-164.38330932474
DeepCCS[M+Na]+138.93130932474
AllCCS[M+H]+125.532859911
AllCCS[M+H-H2O]+120.832859911
AllCCS[M+NH4]+129.832859911
AllCCS[M+Na]+131.132859911
AllCCS[M-H]-125.332859911
AllCCS[M+Na-2H]-128.532859911
AllCCS[M+HCOO]-132.032859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
RHODANINEO=C1CSC(=S)N12499.6Standard polar33892256
RHODANINEO=C1CSC(=S)N11223.4Standard non polar33892256
RHODANINEO=C1CSC(=S)N11599.7Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
RHODANINE,1TMS,isomer #1C[Si](C)(C)N1C(=O)CSC1=S1600.8Semi standard non polar33892256
RHODANINE,1TMS,isomer #1C[Si](C)(C)N1C(=O)CSC1=S1500.8Standard non polar33892256
RHODANINE,1TMS,isomer #1C[Si](C)(C)N1C(=O)CSC1=S2479.2Standard polar33892256
RHODANINE,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)N1C(=O)CSC1=S1799.3Semi standard non polar33892256
RHODANINE,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)N1C(=O)CSC1=S1781.9Standard non polar33892256
RHODANINE,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)N1C(=O)CSC1=S2458.5Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Rhodanine GC-MS (Non-derivatized) - 70eV, Positivesplash10-001i-9600000000-35e48b9913d839fe624c2021-09-23Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Rhodanine 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 ID1013337
KEGG Compound IDC07280
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 ]