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Showing metabocard for Thiomorpholine 1,1-dioxide (HMDB0259018)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 20:55:13 UTC
Update Date2021-09-26 23:16:18 UTC
HMDB IDHMDB0259018
Secondary Accession NumbersNone
Metabolite Identification
Common NameThiomorpholine 1,1-dioxide
DescriptionThiomorpholine 1,1-dioxide 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 a small amount of articles have been published on Thiomorpholine 1,1-dioxide. This compound has been identified in human blood as reported by (PMID: 31557052 ). Thiomorpholine 1,1-dioxide is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Thiomorpholine 1,1-dioxide 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 HMDB0259018 (Thiomorpholine 1,1-dioxide)


  Mrv1652309112122552D          

  8  8  0  0  0  0            999 V2000
    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 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.1842    1.8695    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2448    1.8695    0.0000 O   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 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    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  2  0  0  0  0
  3  5  2  0  0  0  0
  3  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  1  8  1  0  0  0  0
M  END
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3D MOL for HMDB0259018 (Thiomorpholine 1,1-dioxide)

HMDB0259018
     RDKit          3D
Thiomorpholine 1,1-dioxide
 17 17  0  0  0  0  0  0  0  0999 V2000
   -1.0113    2.6397   -0.0335 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4397    1.3367    0.3551 S   0  0  0  0  0  6  0  0  0  0  0  0
    0.0368    1.2935    1.7850 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9859    0.8941   -0.6466 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5120   -0.3926   -0.0162 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5017   -1.3097    0.3388 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7384   -1.2023   -0.3327 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5816   -0.0155    0.1537 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7133    0.7231   -1.6918 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7332    1.6925   -0.5490 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0287   -0.0589    0.9296 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2762   -0.8494   -0.6624 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3798   -1.5158    1.3363 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6241   -1.1228   -1.4209 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3497   -2.1109   -0.0780 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3462    0.2520   -0.5872 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0765   -0.2537    1.1198 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  2  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  2  1  0
  4  9  1  0
  4 10  1  0
  5 11  1  0
  5 12  1  0
  6 13  1  0
  7 14  1  0
  7 15  1  0
  8 16  1  0
  8 17  1  0
M  END
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3D SDF for HMDB0259018 (Thiomorpholine 1,1-dioxide)


  Mrv1652309112122552D          

  8  8  0  0  0  0            999 V2000
    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 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.1842    1.8695    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2448    1.8695    0.0000 O   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 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    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  2  0  0  0  0
  3  5  2  0  0  0  0
  3  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  1  8  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0259018

> <DATABASE_NAME>
hmdb

> <SMILES>
O=S1(=O)CCNCC1

> <INCHI_IDENTIFIER>
InChI=1S/C4H9NO2S/c6-8(7)3-1-5-2-4-8/h5H,1-4H2

> <INCHI_KEY>
NDOVLWQBFFJETK-UHFFFAOYSA-N

> <FORMULA>
C4H9NO2S

> <MOLECULAR_WEIGHT>
135.18

> <EXACT_MASS>
135.035399708

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
17

> <JCHEM_AVERAGE_POLARIZABILITY>
12.666441172599317

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1lambda6-thiomorpholine-1,1-dione

> <ALOGPS_LOGP>
-1.50

> <JCHEM_LOGP>
-1.5325216663333334

> <ALOGPS_LOGS>
0.18

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
5.271452581063801

> <JCHEM_POLAR_SURFACE_AREA>
46.17

> <JCHEM_REFRACTIVITY>
30.295200000000005

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.04e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1lambda6-thiomorpholine-1,1-dione

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0259018 (Thiomorpholine 1,1-dioxide)

HMDB0259018
     RDKit          3D
Thiomorpholine 1,1-dioxide
 17 17  0  0  0  0  0  0  0  0999 V2000
   -1.0113    2.6397   -0.0335 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4397    1.3367    0.3551 S   0  0  0  0  0  6  0  0  0  0  0  0
    0.0368    1.2935    1.7850 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9859    0.8941   -0.6466 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5120   -0.3926   -0.0162 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5017   -1.3097    0.3388 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7384   -1.2023   -0.3327 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5816   -0.0155    0.1537 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7133    0.7231   -1.6918 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7332    1.6925   -0.5490 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0287   -0.0589    0.9296 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2762   -0.8494   -0.6624 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3798   -1.5158    1.3363 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6241   -1.1228   -1.4209 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3497   -2.1109   -0.0780 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3462    0.2520   -0.5872 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0765   -0.2537    1.1198 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  2  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  2  1  0
  4  9  1  0
  4 10  1  0
  5 11  1  0
  5 12  1  0
  6 13  1  0
  7 14  1  0
  7 15  1  0
  8 16  1  0
  8 17  1  0
M  END
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PDB for HMDB0259018 (Thiomorpholine 1,1-dioxide)

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       0.000  -0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    3  S   UNK     0       1.334   2.310   0.000  0.00  0.00           S+0
HETATM    4  O   UNK     0       0.344   3.490   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0       2.324   3.490   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0       1.334  -0.770   0.000  0.00  0.00           N+0
CONECT    1    2    8                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4    5    6                                             
CONECT    4    3                                                            
CONECT    5    3                                                            
CONECT    6    3    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    1                                                       
MASTER        0    0    0    0    0    0    0    0    8    0   16    0
END
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3D PDB for HMDB0259018 (Thiomorpholine 1,1-dioxide)

COMPND    HMDB0259018
HETATM    1  O1  UNL     1      -1.011   2.640  -0.033  1.00  0.00           O  
HETATM    2  S1  UNL     1      -0.440   1.337   0.355  1.00  0.00           S  
HETATM    3  O2  UNL     1       0.037   1.293   1.785  1.00  0.00           O  
HETATM    4  C1  UNL     1       0.986   0.894  -0.647  1.00  0.00           C  
HETATM    5  C2  UNL     1       1.512  -0.393  -0.016  1.00  0.00           C  
HETATM    6  N1  UNL     1       0.502  -1.310   0.339  1.00  0.00           N  
HETATM    7  C3  UNL     1      -0.738  -1.202  -0.333  1.00  0.00           C  
HETATM    8  C4  UNL     1      -1.582  -0.016   0.154  1.00  0.00           C  
HETATM    9  H1  UNL     1       0.713   0.723  -1.692  1.00  0.00           H  
HETATM   10  H2  UNL     1       1.733   1.693  -0.549  1.00  0.00           H  
HETATM   11  H3  UNL     1       2.029  -0.059   0.930  1.00  0.00           H  
HETATM   12  H4  UNL     1       2.276  -0.849  -0.662  1.00  0.00           H  
HETATM   13  H5  UNL     1       0.380  -1.516   1.336  1.00  0.00           H  
HETATM   14  H6  UNL     1      -0.624  -1.123  -1.421  1.00  0.00           H  
HETATM   15  H7  UNL     1      -1.350  -2.111  -0.078  1.00  0.00           H  
HETATM   16  H8  UNL     1      -2.346   0.252  -0.587  1.00  0.00           H  
HETATM   17  H9  UNL     1      -2.077  -0.254   1.120  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    3    4    8
CONECT    4    5    9   10
CONECT    5    6   11   12
CONECT    6    7   13
CONECT    7    8   14   15
CONECT    8   16   17
END
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SMILES for HMDB0259018 (Thiomorpholine 1,1-dioxide)

O=S1(=O)CCNCC1
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INCHI for HMDB0259018 (Thiomorpholine 1,1-dioxide)

InChI=1S/C4H9NO2S/c6-8(7)3-1-5-2-4-8/h5H,1-4H2
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View in JSmolView Stereo Labels
SynonymsNot Available
Chemical FormulaC4H9NO2S
Average Molecular Weight135.18
Monoisotopic Molecular Weight135.035399708
IUPAC Name1lambda6-thiomorpholine-1,1-dione
Traditional Name1lambda6-thiomorpholine-1,1-dione
CAS Registry NumberNot Available
SMILES
O=S1(=O)CCNCC1
InChI Identifier
InChI=1S/C4H9NO2S/c6-8(7)3-1-5-2-4-8/h5H,1-4H2
InChI KeyNDOVLWQBFFJETK-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
  • Sulfone
  • Azacycle
  • Secondary amine
  • Secondary aliphatic amine
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organonitrogen compound
  • Amine
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
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
logP-1.5ALOGPS
logP-1.5ChemAxon
logS0.18ALOGPS
pKa (Strongest Basic)5.27ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area46.17 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity30.3 m³·mol⁻¹ChemAxon
Polarizability12.67 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+125.31530932474
DeepCCS[M-H]-122.91830932474
DeepCCS[M-2H]-158.6530932474
DeepCCS[M+Na]+133.6530932474
AllCCS[M+H]+128.632859911
AllCCS[M+H-H2O]+124.032859911
AllCCS[M+NH4]+133.032859911
AllCCS[M+Na]+134.332859911
AllCCS[M-H]-124.632859911
AllCCS[M+Na-2H]-127.432859911
AllCCS[M+HCOO]-130.432859911

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. 2.72 minutes32390414
Predicted by Siyang on May 30, 20227.9844 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20223.83 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid606.0 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid296.1 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid64.6 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid191.3 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid56.5 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid243.9 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 Acid234.2 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)655.4 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid540.1 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid39.0 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid754.8 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid199.0 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid207.1 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate555.5 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA370.9 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water182.4 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
Thiomorpholine 1,1-dioxideO=S1(=O)CCNCC12297.9Standard polar33892256
Thiomorpholine 1,1-dioxideO=S1(=O)CCNCC11301.2Standard non polar33892256
Thiomorpholine 1,1-dioxideO=S1(=O)CCNCC11284.3Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Thiomorpholine 1,1-dioxide,1TMS,isomer #1C[Si](C)(C)N1CCS(=O)(=O)CC11491.2Semi standard non polar33892256
Thiomorpholine 1,1-dioxide,1TMS,isomer #1C[Si](C)(C)N1CCS(=O)(=O)CC11385.9Standard non polar33892256
Thiomorpholine 1,1-dioxide,1TMS,isomer #1C[Si](C)(C)N1CCS(=O)(=O)CC12385.8Standard polar33892256
Thiomorpholine 1,1-dioxide,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)N1CCS(=O)(=O)CC11752.7Semi standard non polar33892256
Thiomorpholine 1,1-dioxide,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)N1CCS(=O)(=O)CC11687.4Standard non polar33892256
Thiomorpholine 1,1-dioxide,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)N1CCS(=O)(=O)CC12669.0Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Thiomorpholine 1,1-dioxide GC-MS (Non-derivatized) - 70eV, Positivesplash10-002f-9000000000-7efd65b5e24d3217ca062021-09-24Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Thiomorpholine 1,1-dioxide 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 ID4984670
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound6484228
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 ]