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Showing metabocard for Cibulins (HMDB0030299)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-11 17:35:59 UTC
Update Date2023-02-21 17:19:31 UTC
HMDB IDHMDB0030299
Secondary Accession Numbers
  • HMDB30299
Metabolite Identification
Common NameCibulins
DescriptionCibulins, also known as propanesulfanol or propanesulphenate, belongs to the class of organic compounds known as s-alkylsulfenates. These are organosulfur compounds containing a sulfenic acid, where the sulfur atom is linked to an alkyl group. They have the general formula RSOH, where R is an alkyl group. Cibulins is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. Based on a literature review very few articles have been published on Cibulins.
Structure
Data?1676999971
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0030299 (Cibulins)


  Mrv0541 05061305082D          

  5  4  0  0  0  0            999 V2000
   -1.6500    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  2  1  0  0  0  0
  5  3  1  0  0  0  0
  5  4  1  0  0  0  0
M  END
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3D MOL for HMDB0030299 (Cibulins)

HMDB0030299
     RDKit          3D
Cibulins
 13 12  0  0  0  0  0  0  0  0999 V2000
   -1.5869    0.4703   -0.2907 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5984   -0.5823    0.1223 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4659   -0.8420   -0.9222 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3043    0.7071   -1.3066 S   0  0  0  0  0  0  0  0  0  0  0  0
    2.7465    0.8734   -0.4203 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1076    1.1133   -1.0725 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5330    0.0509   -0.6869 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7702    1.1571    0.5704 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0837   -1.5618    0.3636 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0363   -0.2744    1.0419 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0919   -1.3771   -1.8068 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2262   -1.4957   -0.4237 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8812    1.7613   -0.0323 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
  1  6  1  0
  1  7  1  0
  1  8  1  0
  2  9  1  0
  2 10  1  0
  3 11  1  0
  3 12  1  0
  5 13  1  0
M  END
Download

3D SDF for HMDB0030299 (Cibulins)


  Mrv0541 05061305082D          

  5  4  0  0  0  0            999 V2000
   -1.6500    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  2  1  0  0  0  0
  5  3  1  0  0  0  0
  5  4  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0030299

> <DATABASE_NAME>
hmdb

> <SMILES>
CCCSO

> <INCHI_IDENTIFIER>
InChI=1S/C3H8OS/c1-2-3-5-4/h4H,2-3H2,1H3

> <INCHI_KEY>
LYNBNVDYPNEWHG-UHFFFAOYSA-N

> <FORMULA>
C3H8OS

> <MOLECULAR_WEIGHT>
92.16

> <EXACT_MASS>
92.029585568

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_AVERAGE_POLARIZABILITY>
10.153083383866747

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
propane-1-SO-thioperoxol

> <ALOGPS_LOGP>
0.41

> <JCHEM_LOGP>
1.305032741

> <ALOGPS_LOGS>
-0.12

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.96568342099615

> <JCHEM_PKA_STRONGEST_BASIC>
-3.251210071656284

> <JCHEM_POLAR_SURFACE_AREA>
20.23

> <JCHEM_REFRACTIVITY>
25.383000000000003

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.98e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
propane-1-SO-thioperoxol

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0030299 (Cibulins)

HMDB0030299
     RDKit          3D
Cibulins
 13 12  0  0  0  0  0  0  0  0999 V2000
   -1.5869    0.4703   -0.2907 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5984   -0.5823    0.1223 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4659   -0.8420   -0.9222 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3043    0.7071   -1.3066 S   0  0  0  0  0  0  0  0  0  0  0  0
    2.7465    0.8734   -0.4203 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1076    1.1133   -1.0725 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5330    0.0509   -0.6869 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7702    1.1571    0.5704 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0837   -1.5618    0.3636 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0363   -0.2744    1.0419 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0919   -1.3771   -1.8068 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2262   -1.4957   -0.4237 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8812    1.7613   -0.0323 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
  1  6  1  0
  1  7  1  0
  1  8  1  0
  2  9  1  0
  2 10  1  0
  3 11  1  0
  3 12  1  0
  5 13  1  0
M  END
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PDB for HMDB0030299 (Cibulins)

HEADER    PROTEIN                                 06-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAY-13         0                                  
HETATM    1  C   UNK     0      -3.080   2.667   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -2.310   1.334   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.770   1.334   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       1.540   0.000   0.000  0.00  0.00           O+0
HETATM    5  S   UNK     0       0.000   0.000   0.000  0.00  0.00           S+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    5                                                       
CONECT    4    5                                                            
CONECT    5    3    4                                                       
MASTER        0    0    0    0    0    0    0    0    5    0    8    0
END
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3D PDB for HMDB0030299 (Cibulins)

COMPND    HMDB0030299
HETATM    1  C1  UNL     1      -1.587   0.470  -0.291  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.598  -0.582   0.122  1.00  0.00           C  
HETATM    3  C3  UNL     1       0.466  -0.842  -0.922  1.00  0.00           C  
HETATM    4  S1  UNL     1       1.304   0.707  -1.307  1.00  0.00           S  
HETATM    5  O1  UNL     1       2.747   0.873  -0.420  1.00  0.00           O  
HETATM    6  H1  UNL     1      -1.108   1.113  -1.072  1.00  0.00           H  
HETATM    7  H2  UNL     1      -2.533   0.051  -0.687  1.00  0.00           H  
HETATM    8  H3  UNL     1      -1.770   1.157   0.570  1.00  0.00           H  
HETATM    9  H4  UNL     1      -1.084  -1.562   0.364  1.00  0.00           H  
HETATM   10  H5  UNL     1      -0.036  -0.274   1.042  1.00  0.00           H  
HETATM   11  H6  UNL     1       0.092  -1.377  -1.807  1.00  0.00           H  
HETATM   12  H7  UNL     1       1.226  -1.496  -0.424  1.00  0.00           H  
HETATM   13  H8  UNL     1       2.881   1.761  -0.032  1.00  0.00           H  
CONECT    1    2    6    7    8
CONECT    2    3    9   10
CONECT    3    4   11   12
CONECT    4    5
CONECT    5   13
END
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SMILES for HMDB0030299 (Cibulins)

CCCSO
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INCHI for HMDB0030299 (Cibulins)

InChI=1S/C3H8OS/c1-2-3-5-4/h4H,2-3H2,1H3
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
PropanesulfanolChEBI
PropanesulphanolGenerator
Alkyl propyl sulfoxidesHMDB
PropanesulfenateHMDB
PropanesulphenateHMDB
Propanesulphenic acidHMDB
CibulinsChEBI
Chemical FormulaC3H8OS
Average Molecular Weight92.16
Monoisotopic Molecular Weight92.029585568
IUPAC Namepropane-1-SO-thioperoxol
Traditional Namepropane-1-SO-thioperoxol
CAS Registry NumberNot Available
SMILES
CCCSO
InChI Identifier
InChI=1S/C3H8OS/c1-2-3-5-4/h4H,2-3H2,1H3
InChI KeyLYNBNVDYPNEWHG-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as s-alkylsulfenates. These are organosulfur compounds containing a sulfenic acid, where the sulfur atom is linked to an alkyl group. They have the general formula RSOH, where R is an alkyl group.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassOrganosulfenic acids and derivatives
Sub ClassOrganosulfenic acids
Direct ParentS-alkylsulfenates
Alternative Parents
Substituents
  • S-alkylsulfenate
  • Sulfenyl compound
  • So-thioperoxol
  • Organic oxygen compound
  • Hydrocarbon derivative
  • Organosulfur compound
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological locationRoute of exposureSource
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
Water Solubility69.8 g/LALOGPS
logP0.41ALOGPS
logP1.31ChemAxon
logS-0.12ALOGPS
pKa (Strongest Acidic)13.97ChemAxon
pKa (Strongest Basic)-3.3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area20.23 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity25.38 m³·mol⁻¹ChemAxon
Polarizability10.15 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+116.07731661259
DarkChem[M-H]-111.68231661259
DeepCCS[M+H]+124.10930932474
DeepCCS[M-H]-122.21530932474
DeepCCS[M-2H]-157.63230932474
DeepCCS[M+Na]+131.83930932474
AllCCS[M+H]+123.132859911
AllCCS[M+H-H2O]+118.732859911
AllCCS[M+NH4]+127.132859911
AllCCS[M+Na]+128.332859911
AllCCS[M-H]-142.432859911
AllCCS[M+Na-2H]-148.032859911
AllCCS[M+HCOO]-154.132859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
CibulinsCCCSO1337.2Standard polar33892256
CibulinsCCCSO796.0Standard non polar33892256
CibulinsCCCSO804.3Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Cibulins,1TMS,isomer #1CCCSO[Si](C)(C)C903.6Semi standard non polar33892256
Cibulins,1TMS,isomer #1CCCSO[Si](C)(C)C937.5Standard non polar33892256
Cibulins,1TBDMS,isomer #1CCCSO[Si](C)(C)C(C)(C)C1137.1Semi standard non polar33892256
Cibulins,1TBDMS,isomer #1CCCSO[Si](C)(C)C(C)(C)C1129.8Standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Cibulins GC-MS (Non-derivatized) - 70eV, Positivesplash10-0007-9000000000-3e0150f90e29e38aa46d2017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Cibulins 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 - Cibulins 10V, Positive-QTOFsplash10-0006-9000000000-ae17e0cfcc95db8e2a122016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cibulins 20V, Positive-QTOFsplash10-0006-9000000000-42b950130e15d8fd3fd62016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cibulins 40V, Positive-QTOFsplash10-0007-9000000000-1fb91a88edbe17e97c6d2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cibulins 10V, Negative-QTOFsplash10-0006-9000000000-e4ccbcb0c8cf004aad7a2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cibulins 20V, Negative-QTOFsplash10-0007-9000000000-35600ec90bbeb64844522016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cibulins 40V, Negative-QTOFsplash10-0002-9000000000-4eabbfbb50c9f079e6872016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cibulins 10V, Negative-QTOFsplash10-0006-9000000000-2014a2c8c09ca0fe13592021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cibulins 20V, Negative-QTOFsplash10-0002-9000000000-53361442fd4c3cbc873c2021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cibulins 40V, Negative-QTOFsplash10-00dj-9000000000-f07710c3da24137276562021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cibulins 10V, Positive-QTOFsplash10-004i-9000000000-1fcbbca34690dbfbc01c2021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cibulins 20V, Positive-QTOFsplash10-004i-9000000000-e06738201cdd358937f52021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cibulins 40V, Positive-QTOFsplash10-0006-9000000000-e6964ab81f61e65c8f9b2021-09-25Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum

IR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M-H]-)2023-02-03FELIX labView Spectrum
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)2023-02-03FELIX labView Spectrum
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)2023-02-03FELIX labView Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB002136
KNApSAcK IDNot Available
Chemspider ID25947238
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound20514207
PDB IDNot Available
ChEBI ID91018
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. (). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .