Hmdb loader

Showing metabocard for Thiiranepropanenitrile (HMDB0038460)

Jump To Section:
IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesXML
Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-11 23:46:48 UTC
Update Date2023-02-21 17:26:36 UTC
HMDB IDHMDB0038460
Secondary Accession Numbers
  • HMDB38460
Metabolite Identification
Common NameThiiranepropanenitrile
DescriptionThiiranepropanenitrile belongs to the class of organic compounds known as thiiranes. These are heterocyclic compounds containing a saturated three-member ring with two carbon atoms and one sulfur atom. Thiiranepropanenitrile has been detected, but not quantified in, brassicas. This could make thiiranepropanenitrile a potential biomarker for the consumption of these foods. Based on a literature review very few articles have been published on Thiiranepropanenitrile.
Structure
Data?1677000396
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0038460 (Thiiranepropanenitrile)


  Mrv0541 05061310282D          

  7  7  0  0  0  0            999 V2000
    0.9526    2.1263    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2382    1.7138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9526    2.9513    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6507    0.1743    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2382    0.8888    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9526    3.7763    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1743    0.1743    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  1  1  0  0  0  0
  5  2  1  0  0  0  0
  5  4  1  0  0  0  0
  6  3  3  0  0  0  0
  7  4  1  0  0  0  0
  7  5  1  0  0  0  0
M  END
Download

3D MOL for HMDB0038460 (Thiiranepropanenitrile)

HMDB0038460
     RDKit          3D
Thiiranepropanenitrile
 14 14  0  0  0  0  0  0  0  0999 V2000
    2.5736    1.7964   -0.1091 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1251    0.7478    0.0871 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5545   -0.5636    0.3345 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1951   -0.6574   -0.3221 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7597    0.3827    0.2145 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1351    0.3397   -0.4028 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1668    1.7701   -0.7841 S   0  0  0  0  0  0  0  0  0  0  0  0
    2.2080   -1.3480   -0.0945 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4719   -0.7681    1.4216 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2584   -0.6538   -1.4183 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2327   -1.6518   -0.0241 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7139    0.5115    1.3211 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0080    0.5237    0.2857 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3706   -0.4292   -1.1716 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  3  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  5  1  0
  3  8  1  0
  3  9  1  0
  4 10  1  0
  4 11  1  0
  5 12  1  0
  6 13  1  0
  6 14  1  0
M  END
Download

3D SDF for HMDB0038460 (Thiiranepropanenitrile)


  Mrv0541 05061310282D          

  7  7  0  0  0  0            999 V2000
    0.9526    2.1263    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2382    1.7138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9526    2.9513    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6507    0.1743    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2382    0.8888    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9526    3.7763    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1743    0.1743    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  1  1  0  0  0  0
  5  2  1  0  0  0  0
  5  4  1  0  0  0  0
  6  3  3  0  0  0  0
  7  4  1  0  0  0  0
  7  5  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0038460

> <DATABASE_NAME>
hmdb

> <SMILES>
N#CCCC1CS1

> <INCHI_IDENTIFIER>
InChI=1S/C5H7NS/c6-3-1-2-5-4-7-5/h5H,1-2,4H2

> <INCHI_KEY>
ZAGXORSINWAUSP-UHFFFAOYSA-N

> <FORMULA>
C5H7NS

> <MOLECULAR_WEIGHT>
113.181

> <EXACT_MASS>
113.029919919

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_AVERAGE_POLARIZABILITY>
12.08517767575896

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-(thiiran-2-yl)propanenitrile

> <ALOGPS_LOGP>
1.28

> <JCHEM_LOGP>
0.6282326616666665

> <ALOGPS_LOGS>
-1.27

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_POLAR_SURFACE_AREA>
23.79

> <JCHEM_REFRACTIVITY>
31.489799999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.11e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-(thiiran-2-yl)propanenitrile

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0038460 (Thiiranepropanenitrile)

HMDB0038460
     RDKit          3D
Thiiranepropanenitrile
 14 14  0  0  0  0  0  0  0  0999 V2000
    2.5736    1.7964   -0.1091 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1251    0.7478    0.0871 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5545   -0.5636    0.3345 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1951   -0.6574   -0.3221 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7597    0.3827    0.2145 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1351    0.3397   -0.4028 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1668    1.7701   -0.7841 S   0  0  0  0  0  0  0  0  0  0  0  0
    2.2080   -1.3480   -0.0945 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4719   -0.7681    1.4216 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2584   -0.6538   -1.4183 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2327   -1.6518   -0.0241 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7139    0.5115    1.3211 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0080    0.5237    0.2857 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3706   -0.4292   -1.1716 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  3  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  5  1  0
  3  8  1  0
  3  9  1  0
  4 10  1  0
  4 11  1  0
  5 12  1  0
  6 13  1  0
  6 14  1  0
M  END
Download

PDB for HMDB0038460 (Thiiranepropanenitrile)

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       1.778   3.969   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.445   3.199   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.778   5.509   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.215   0.325   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.445   1.659   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0       1.778   7.049   0.000  0.00  0.00           N+0
HETATM    7  S   UNK     0      -0.325   0.325   0.000  0.00  0.00           S+0
CONECT    1    2    3                                                       
CONECT    2    1    5                                                       
CONECT    3    1    6                                                       
CONECT    4    5    7                                                       
CONECT    5    2    4    7                                                  
CONECT    6    3                                                            
CONECT    7    4    5                                                       
MASTER        0    0    0    0    0    0    0    0    7    0   14    0
END
Download

3D PDB for HMDB0038460 (Thiiranepropanenitrile)

COMPND    HMDB0038460
HETATM    1  N1  UNL     1       2.574   1.796  -0.109  1.00  0.00           N  
HETATM    2  C1  UNL     1       2.125   0.748   0.087  1.00  0.00           C  
HETATM    3  C2  UNL     1       1.555  -0.564   0.334  1.00  0.00           C  
HETATM    4  C3  UNL     1       0.195  -0.657  -0.322  1.00  0.00           C  
HETATM    5  C4  UNL     1      -0.760   0.383   0.215  1.00  0.00           C  
HETATM    6  C5  UNL     1      -2.135   0.340  -0.403  1.00  0.00           C  
HETATM    7  S1  UNL     1      -1.167   1.770  -0.784  1.00  0.00           S  
HETATM    8  H1  UNL     1       2.208  -1.348  -0.095  1.00  0.00           H  
HETATM    9  H2  UNL     1       1.472  -0.768   1.422  1.00  0.00           H  
HETATM   10  H3  UNL     1       0.258  -0.654  -1.418  1.00  0.00           H  
HETATM   11  H4  UNL     1      -0.233  -1.652  -0.024  1.00  0.00           H  
HETATM   12  H5  UNL     1      -0.714   0.512   1.321  1.00  0.00           H  
HETATM   13  H6  UNL     1      -3.008   0.524   0.286  1.00  0.00           H  
HETATM   14  H7  UNL     1      -2.371  -0.429  -1.172  1.00  0.00           H  
CONECT    1    2    2    2
CONECT    2    3
CONECT    3    4    8    9
CONECT    4    5   10   11
CONECT    5    6    7   12
CONECT    6    7   13   14
END
Download

SMILES for HMDB0038460 (Thiiranepropanenitrile)

N#CCCC1CS1
Download

INCHI for HMDB0038460 (Thiiranepropanenitrile)

InChI=1S/C5H7NS/c6-3-1-2-5-4-7-5/h5H,1-2,4H2
Download
View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
(+-)-ThIIranepropanenitrileHMDB
1-cyano-3,4-EpithiobutaneHMDB, MeSH
4,5-epithio-ValeronitrileHMDB
4,5-EpithiovaleronitrileHMDB
cyano-3,4-EPITHIOBUTANEHMDB
Thiiranepropanenitrile, 9ciHMDB
ThiiranepropanenitrileMeSH
1-Cyano-3,4-epithiobutane, (+-)-isomerMeSH
Chemical FormulaC5H7NS
Average Molecular Weight113.181
Monoisotopic Molecular Weight113.029919919
IUPAC Name3-(thiiran-2-yl)propanenitrile
Traditional Name3-(thiiran-2-yl)propanenitrile
CAS Registry Number54096-45-6
SMILES
N#CCCC1CS1
InChI Identifier
InChI=1S/C5H7NS/c6-3-1-2-5-4-7-5/h5H,1-2,4H2
InChI KeyZAGXORSINWAUSP-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as thiiranes. These are heterocyclic compounds containing a saturated three-member ring with two carbon atoms and one sulfur atom.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassThiiranes
Sub ClassNot Available
Direct ParentThiiranes
Alternative Parents
Substituents
  • Dialkylthioether
  • Thioether
  • Thiirane
  • Nitrile
  • Carbonitrile
  • Organic nitrogen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Organonitrogen compound
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological locationRoute of exposureSource
ProcessNot Available
Role
Biological role
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water Solubility13520 mg/L @ 25 °C (est)The Good Scents Company Information System
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility6.11 g/LALOGPS
logP1.28ALOGPS
logP0.63ChemAxon
logS-1.3ALOGPS
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area23.79 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity31.49 m³·mol⁻¹ChemAxon
Polarizability12.09 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
DarkChem[M+H]+122.37631661259
DarkChem[M-H]-117.39431661259
DeepCCS[M+H]+128.56530932474
DeepCCS[M-H]-126.46730932474
DeepCCS[M-2H]-162.00830932474
DeepCCS[M+Na]+136.50730932474
AllCCS[M+H]+122.632859911
AllCCS[M+H-H2O]+118.132859911
AllCCS[M+NH4]+126.932859911
AllCCS[M+Na]+128.132859911
AllCCS[M-H]-128.132859911
AllCCS[M+Na-2H]-131.132859911
AllCCS[M+HCOO]-134.532859911

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, 2022.2.7 minutes32390414
Predicted by Siyang on May 30, 202212.9328 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20222.22 minutes32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid74.9 seconds40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid1737.2 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid487.4 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid172.7 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid344.0 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid187.7 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid476.7 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 Acid605.8 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)234.8 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid1025.9 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid333.4 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid1080.2 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid328.7 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid366.8 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate561.3 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA505.6 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water216.3 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
ThiiranepropanenitrileN#CCCC1CS11913.5Standard polar33892256
ThiiranepropanenitrileN#CCCC1CS11037.5Standard non polar33892256
ThiiranepropanenitrileN#CCCC1CS11128.5Semi standard non polar33892256
Spectra
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 IDFDB017819
KNApSAcK IDC00054741
Chemspider ID90879
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound100582
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1632241
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.. .