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Showing metabocard for Thiomorpholine (HMDB0259017)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 20:55:08 UTC
Update Date2021-09-26 23:16:18 UTC
HMDB IDHMDB0259017
Secondary Accession NumbersNone
Metabolite Identification
Common NameThiomorpholine
Descriptionthiomorpholine, also known as 1,4-thiazan or parathiazan, belongs to the class of organic compounds known as thiomorpholines. These are heterocyclic compounds containing a thiomorpholine ring, which is a six-membered aliphatic ring containing one nitrogen atom and one sulfur atom at positions 1 and 4 respectively, and four carbon atoms. Based on a literature review very few articles have been published on thiomorpholine. This compound has been identified in human blood as reported by (PMID: 31557052 ). Thiomorpholine is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Thiomorpholine 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 HMDB0259017 (Thiomorpholine)


  Mrv1652309112122552D          

  6  6  0  0  0  0            999 V2000
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  1  6  1  0  0  0  0
M  END
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3D MOL for HMDB0259017 (Thiomorpholine)

HMDB0259017
     RDKit          3D
Thiomorpholine
 15 15  0  0  0  0  0  0  0  0999 V2000
   -1.3157   -0.0075   -0.0455 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9050    1.3509    0.4000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8620    1.5088    0.7233 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.7565    0.1182   -0.0603 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7778   -1.0607    0.0157 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3241   -0.6544   -0.8551 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5302   -0.6959    0.8149 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2521    0.0793   -0.6464 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2096    2.0837   -0.3804 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4281    1.5536    1.3773 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8645    0.3320   -1.1548 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7053   -0.0948    0.4247 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4215   -1.0724    1.0808 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2400   -1.9997   -0.2851 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6627   -1.4411   -1.4092 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  6  1  0
  6  1  1  0
  1  7  1  0
  1  8  1  0
  2  9  1  0
  2 10  1  0
  4 11  1  0
  4 12  1  0
  5 13  1  0
  5 14  1  0
  6 15  1  0
M  END
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3D SDF for HMDB0259017 (Thiomorpholine)


  Mrv1652309112122552D          

  6  6  0  0  0  0            999 V2000
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  1  6  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0259017

> <DATABASE_NAME>
hmdb

> <SMILES>
C1CSCCN1

> <INCHI_IDENTIFIER>
InChI=1S/C4H9NS/c1-3-6-4-2-5-1/h5H,1-4H2

> <INCHI_KEY>
BRNULMACUQOKMR-UHFFFAOYSA-N

> <FORMULA>
C4H9NS

> <MOLECULAR_WEIGHT>
103.18

> <EXACT_MASS>
103.045570468

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
15

> <JCHEM_AVERAGE_POLARIZABILITY>
11.268886111177332

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
thiomorpholine

> <ALOGPS_LOGP>
0.17

> <JCHEM_LOGP>
0.16828029466666677

> <ALOGPS_LOGS>
-0.29

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_BASIC>
9.330078396593548

> <JCHEM_POLAR_SURFACE_AREA>
12.03

> <JCHEM_REFRACTIVITY>
30.0535

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.27e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
thiomorpholine

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0259017 (Thiomorpholine)

HMDB0259017
     RDKit          3D
Thiomorpholine
 15 15  0  0  0  0  0  0  0  0999 V2000
   -1.3157   -0.0075   -0.0455 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9050    1.3509    0.4000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8620    1.5088    0.7233 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.7565    0.1182   -0.0603 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7778   -1.0607    0.0157 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3241   -0.6544   -0.8551 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5302   -0.6959    0.8149 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2521    0.0793   -0.6464 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2096    2.0837   -0.3804 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4281    1.5536    1.3773 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8645    0.3320   -1.1548 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7053   -0.0948    0.4247 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4215   -1.0724    1.0808 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2400   -1.9997   -0.2851 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6627   -1.4411   -1.4092 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  6  1  0
  6  1  1  0
  1  7  1  0
  1  8  1  0
  2  9  1  0
  2 10  1  0
  4 11  1  0
  4 12  1  0
  5 13  1  0
  5 14  1  0
  6 15  1  0
M  END
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PDB for HMDB0259017 (Thiomorpholine)

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       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    3  S   UNK     0       2.667  -0.000   0.000  0.00  0.00           S+0
HETATM    4  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0       0.000   1.540   0.000  0.00  0.00           N+0
CONECT    1    2    6                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    1                                                       
MASTER        0    0    0    0    0    0    0    0    6    0   12    0
END
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3D PDB for HMDB0259017 (Thiomorpholine)

COMPND    HMDB0259017
HETATM    1  C1  UNL     1      -1.316  -0.008  -0.045  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.905   1.351   0.400  1.00  0.00           C  
HETATM    3  S1  UNL     1       0.862   1.509   0.723  1.00  0.00           S  
HETATM    4  C3  UNL     1       1.757   0.118  -0.060  1.00  0.00           C  
HETATM    5  C4  UNL     1       0.778  -1.061   0.016  1.00  0.00           C  
HETATM    6  N1  UNL     1      -0.324  -0.654  -0.855  1.00  0.00           N  
HETATM    7  H1  UNL     1      -1.530  -0.696   0.815  1.00  0.00           H  
HETATM    8  H2  UNL     1      -2.252   0.079  -0.646  1.00  0.00           H  
HETATM    9  H3  UNL     1      -1.210   2.084  -0.380  1.00  0.00           H  
HETATM   10  H4  UNL     1      -1.428   1.554   1.377  1.00  0.00           H  
HETATM   11  H5  UNL     1       1.864   0.332  -1.155  1.00  0.00           H  
HETATM   12  H6  UNL     1       2.705  -0.095   0.425  1.00  0.00           H  
HETATM   13  H7  UNL     1       0.421  -1.072   1.081  1.00  0.00           H  
HETATM   14  H8  UNL     1       1.240  -2.000  -0.285  1.00  0.00           H  
HETATM   15  H9  UNL     1      -0.663  -1.441  -1.409  1.00  0.00           H  
CONECT    1    2    6    7    8
CONECT    2    3    9   10
CONECT    3    4
CONECT    4    5   11   12
CONECT    5    6   13   14
CONECT    6   15
END
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SMILES for HMDB0259017 (Thiomorpholine)

C1CSCCN1
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INCHI for HMDB0259017 (Thiomorpholine)

InChI=1S/C4H9NS/c1-3-6-4-2-5-1/h5H,1-4H2
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View in JSmolView Stereo Labels
Synonyms
ValueSource
1,4-ThiazanChEBI
1,4-ThiazaneChEBI
1-Thia-4-azacyclohexaneChEBI
ParathiazanChEBI
Tetrahydro-1,4-thiazineChEBI
ThiamorpholineChEBI
ThiazolidinaneChEBI
Thiamorpholine hydrochlorideMeSH
Chemical FormulaC4H9NS
Average Molecular Weight103.18
Monoisotopic Molecular Weight103.045570468
IUPAC Namethiomorpholine
Traditional Namethiomorpholine
CAS Registry NumberNot Available
SMILES
C1CSCCN1
InChI Identifier
InChI=1S/C4H9NS/c1-3-6-4-2-5-1/h5H,1-4H2
InChI KeyBRNULMACUQOKMR-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as thiomorpholines. These are heterocyclic compounds containing a thiomorpholine ring, which is a six-membered aliphatic ring containing one nitrogen atom and one sulfur atom at positions 1 and 4 respectively, and four carbon atoms.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassThiazinanes
Sub ClassThiomorpholines
Direct ParentThiomorpholines
Alternative Parents
Substituents
  • 1,4-thiazinane
  • Azacycle
  • Dialkylthioether
  • 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
Not AvailableNot 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
logP0.17ALOGPS
logP0.17ChemAxon
logS-0.29ALOGPS
pKa (Strongest Basic)9.33ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area12.03 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity30.05 m³·mol⁻¹ChemAxon
Polarizability11.27 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]+124.26630932474
DeepCCS[M-H]-121.76630932474
DeepCCS[M-2H]-157.8130932474
DeepCCS[M+Na]+132.31630932474
AllCCS[M+H]+119.332859911
AllCCS[M+H-H2O]+114.332859911
AllCCS[M+NH4]+124.032859911
AllCCS[M+Na]+125.332859911
AllCCS[M-H]-126.532859911
AllCCS[M+Na-2H]-130.432859911
AllCCS[M+HCOO]-134.732859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
ThiomorpholineC1CSCCN11562.2Standard polar33892256
ThiomorpholineC1CSCCN1934.9Standard non polar33892256
ThiomorpholineC1CSCCN1966.3Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Thiomorpholine,1TMS,isomer #1C[Si](C)(C)N1CCSCC11115.3Semi standard non polar33892256
Thiomorpholine,1TMS,isomer #1C[Si](C)(C)N1CCSCC11120.8Standard non polar33892256
Thiomorpholine,1TMS,isomer #1C[Si](C)(C)N1CCSCC11767.9Standard polar33892256
Thiomorpholine,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)N1CCSCC11344.5Semi standard non polar33892256
Thiomorpholine,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)N1CCSCC11340.1Standard non polar33892256
Thiomorpholine,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)N1CCSCC12005.3Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Thiomorpholine GC-MS (Non-derivatized) - 70eV, Positivesplash10-0gvo-9100000000-ada1de03ad188dae38392021-09-23Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Thiomorpholine 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 ID60509
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkThiomorpholine
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI ID36392
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 ]