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Showing metabocard for Tetramethylene sulfoxide (HMDB0258917)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 20:45:19 UTC
Update Date2021-09-26 23:16:09 UTC
HMDB IDHMDB0258917
Secondary Accession NumbersNone
Metabolite Identification
Common NameTetramethylene sulfoxide
Description1λ⁴-thiolan-1-one belongs to the class of organic compounds known as thiolanes. These are organic compounds containing thiolane, a five-member saturated ring containing four carbon atoms and a sulfur atom. 1λ⁴-thiolan-1-one exists in all living organisms, ranging from bacteria to humans. Based on a literature review very few articles have been published on 1λ⁴-thiolan-1-one. This compound has been identified in human blood as reported by (PMID: 31557052 ). Tetramethylene sulfoxide is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Tetramethylene sulfoxide 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 HMDB0258917 (Tetramethylene sulfoxide)

Structure #1
  Mrv0541 02241207352D          

  6  6  0  0  0  0            999 V2000
    0.9802   -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
    1.2351    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.9392    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1142    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  2  4  1  0  0  0  0
  3  6  1  0  0  0  0
  4  6  1  0  0  0  0
  5  6  2  0  0  0  0
M  END
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3D MOL for HMDB0258917 (Tetramethylene sulfoxide)

HMDB0258917
     RDKit          3D
Tetramethylene sulfoxide
 14 14  0  0  0  0  0  0  0  0999 V2000
    0.0686    2.8299    0.4638 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0283    1.4393    0.4462 S   0  0  0  0  0  4  0  0  0  0  0  0
    1.3694    0.3601    0.2266 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6062   -0.9761    0.1888 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6439   -0.7225   -0.6298 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3594    0.4602    0.0444 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8242    0.4823   -0.7776 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0969    0.2749    1.0377 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3451   -1.3213    1.1870 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2165   -1.6960   -0.3436 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3829   -0.4586   -1.6630 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2797   -1.5991   -0.5282 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0759    0.8782   -0.6629 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8134    0.0487    0.9628 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  1  0
  6  2  1  0
  3  7  1  0
  3  8  1  0
  4  9  1  0
  4 10  1  0
  5 11  1  0
  5 12  1  0
  6 13  1  0
  6 14  1  0
M  END
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3D SDF for HMDB0258917 (Tetramethylene sulfoxide)

Structure #1
  Mrv0541 02241207352D          

  6  6  0  0  0  0            999 V2000
    0.9802   -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
    1.2351    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.9392    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1142    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  2  4  1  0  0  0  0
  3  6  1  0  0  0  0
  4  6  1  0  0  0  0
  5  6  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0258917

> <DATABASE_NAME>
hmdb

> <SMILES>
O=S1CCCC1

> <INCHI_IDENTIFIER>
InChI=1S/C4H8OS/c5-6-3-1-2-4-6/h1-4H2

> <INCHI_KEY>
ISXOBTBCNRIIQO-UHFFFAOYSA-N

> <FORMULA>
C4H8OS

> <MOLECULAR_WEIGHT>
104.171

> <EXACT_MASS>
104.029585568

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_AVERAGE_POLARIZABILITY>
10.733542090417647

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1λ⁴-thiolan-1-one

> <ALOGPS_LOGP>
0.06

> <JCHEM_LOGP>
-0.6976897453333334

> <ALOGPS_LOGS>
-0.30

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-6.391712170486993

> <JCHEM_POLAR_SURFACE_AREA>
17.07

> <JCHEM_REFRACTIVITY>
28.210800000000003

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.17e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
tetramethylene sulfoxide

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0258917 (Tetramethylene sulfoxide)

HMDB0258917
     RDKit          3D
Tetramethylene sulfoxide
 14 14  0  0  0  0  0  0  0  0999 V2000
    0.0686    2.8299    0.4638 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0283    1.4393    0.4462 S   0  0  0  0  0  4  0  0  0  0  0  0
    1.3694    0.3601    0.2266 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6062   -0.9761    0.1888 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6439   -0.7225   -0.6298 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3594    0.4602    0.0444 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8242    0.4823   -0.7776 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0969    0.2749    1.0377 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3451   -1.3213    1.1870 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2165   -1.6960   -0.3436 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3829   -0.4586   -1.6630 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2797   -1.5991   -0.5282 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0759    0.8782   -0.6629 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8134    0.0487    0.9628 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  1  0
  6  2  1  0
  3  7  1  0
  3  8  1  0
  4  9  1  0
  4 10  1  0
  5 11  1  0
  5 12  1  0
  6 13  1  0
  6 14  1  0
M  END
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PDB for HMDB0258917 (Tetramethylene sulfoxide)

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: Structure #1                                      
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         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  C   UNK     0       2.306   1.175   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.186   1.175   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       1.060   3.620   0.000  0.00  0.00           O+0
HETATM    6  S   UNK     0       1.060   2.080   0.000  0.00  0.00           S+0
CONECT    1    2    3                                                       
CONECT    2    1    4                                                       
CONECT    3    1    6                                                       
CONECT    4    2    6                                                       
CONECT    5    6                                                            
CONECT    6    3    4    5                                                  
MASTER        0    0    0    0    0    0    0    0    6    0   12    0
END
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3D PDB for HMDB0258917 (Tetramethylene sulfoxide)

COMPND    HMDB0258917
HETATM    1  O1  UNL     1       0.069   2.830   0.464  1.00  0.00           O  
HETATM    2  S1  UNL     1       0.028   1.439   0.446  1.00  0.00           S  
HETATM    3  C1  UNL     1       1.369   0.360   0.227  1.00  0.00           C  
HETATM    4  C2  UNL     1       0.606  -0.976   0.189  1.00  0.00           C  
HETATM    5  C3  UNL     1      -0.644  -0.722  -0.630  1.00  0.00           C  
HETATM    6  C4  UNL     1      -1.359   0.460   0.044  1.00  0.00           C  
HETATM    7  H1  UNL     1       1.824   0.482  -0.778  1.00  0.00           H  
HETATM    8  H2  UNL     1       2.097   0.275   1.038  1.00  0.00           H  
HETATM    9  H3  UNL     1       0.345  -1.321   1.187  1.00  0.00           H  
HETATM   10  H4  UNL     1       1.216  -1.696  -0.344  1.00  0.00           H  
HETATM   11  H5  UNL     1      -0.383  -0.459  -1.663  1.00  0.00           H  
HETATM   12  H6  UNL     1      -1.280  -1.599  -0.528  1.00  0.00           H  
HETATM   13  H7  UNL     1      -2.076   0.878  -0.663  1.00  0.00           H  
HETATM   14  H8  UNL     1      -1.813   0.049   0.963  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    6
CONECT    3    4    7    8
CONECT    4    5    9   10
CONECT    5    6   11   12
CONECT    6   13   14
END
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SMILES for HMDB0258917 (Tetramethylene sulfoxide)

O=S1CCCC1
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INCHI for HMDB0258917 (Tetramethylene sulfoxide)

InChI=1S/C4H8OS/c5-6-3-1-2-4-6/h1-4H2
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View in JSmolView Stereo Labels
Synonyms
ValueSource
tetrahydro-Thiophene-1-oxideChEMBL
TETRAMETHYLENE sulphoxideGenerator
Tetrahydrothiophene 1-oxideMeSH
Tetramethylene sulfoxideMeSH
Chemical FormulaC4H8OS
Average Molecular Weight104.171
Monoisotopic Molecular Weight104.029585568
IUPAC Name1λ⁴-thiolan-1-one
Traditional Nametetramethylene sulfoxide
CAS Registry NumberNot Available
SMILES
O=S1CCCC1
InChI Identifier
InChI=1S/C4H8OS/c5-6-3-1-2-4-6/h1-4H2
InChI KeyISXOBTBCNRIIQO-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as thiolanes. These are organic compounds containing thiolane, a five-member saturated ring containing four carbon atoms and a sulfur atom.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassThiolanes
Sub ClassNot Available
Direct ParentThiolanes
Alternative Parents
Substituents
  • Thiolane
  • Sulfoxide
  • Sulfinyl compound
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • 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
PropertyValueSource
logP0.06ALOGPS
logP-0.7ChemAxon
logS-0.3ALOGPS
pKa (Strongest Basic)-6.4ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area17.07 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity28.21 m³·mol⁻¹ChemAxon
Polarizability10.73 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]+121.90830932474
DeepCCS[M-H]-119.96830932474
DeepCCS[M-2H]-155.35530932474
DeepCCS[M+Na]+129.72730932474
AllCCS[M+H]+120.332859911
AllCCS[M+H-H2O]+115.332859911
AllCCS[M+NH4]+125.032859911
AllCCS[M+Na]+126.332859911
AllCCS[M-H]-124.932859911
AllCCS[M+Na-2H]-128.732859911
AllCCS[M+HCOO]-132.832859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.3.14 minutes32390414
Predicted by Siyang on May 30, 20228.0086 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20221.68 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid921.6 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid314.4 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid95.7 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid217.4 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid78.0 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid244.0 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 Acid269.0 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)375.5 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid603.0 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid139.4 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid688.5 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid208.4 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid245.1 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate564.2 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA293.1 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water180.0 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
Tetramethylene sulfoxideO=S1CCCC11483.5Standard polar33892256
Tetramethylene sulfoxideO=S1CCCC1942.6Standard non polar33892256
Tetramethylene sulfoxideO=S1CCCC1988.0Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Tetramethylene sulfoxide GC-MS (Non-derivatized) - 70eV, Positivesplash10-056u-9000000000-f4e04aa72428fbce8bbd2021-09-24Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Tetramethylene sulfoxide GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Tetramethylene sulfoxide 10V, Positive-QTOFsplash10-0a4i-1900000000-7c2ac4d8596be6ae12f32019-02-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Tetramethylene sulfoxide 20V, Positive-QTOFsplash10-0006-9000000000-6661ca56f627b32c31a82019-02-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Tetramethylene sulfoxide 40V, Positive-QTOFsplash10-004r-9000000000-073a292ffce8103417482019-02-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Tetramethylene sulfoxide 10V, Negative-QTOFsplash10-0udi-4900000000-0c72b7a51e770c1b3d132019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Tetramethylene sulfoxide 20V, Negative-QTOFsplash10-0udi-4900000000-3eeccc8d5bf2e38103f22019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Tetramethylene sulfoxide 40V, Negative-QTOFsplash10-000l-9000000000-38c96a53fcb1c1e82d902019-02-23Wishart 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 ID1096
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 ]