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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-11 17:51:12 UTC

Update Date

2023-02-21 17:22:35 UTC

HMDB ID

HMDB0032688

Secondary Accession Numbers

HMDB32688

Metabolite Identification

Common Name

(Z)-1-(Methylthio)-5-phenyl-1-penten-3-yne

Description

(Z)-1-(Methylthio)-5-phenyl-1-penten-3-yne belongs to the class of organic compounds known as benzene and substituted derivatives. These are aromatic compounds containing one monocyclic ring system consisting of benzene. Based on a literature review very few articles have been published on (Z)-1-(Methylthio)-5-phenyl-1-penten-3-yne.

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

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      -5.335   3.080   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.334   5.390   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.667   0.000   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  C   UNK     0       0.000   4.620   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -2.667   6.160   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -4.001   5.390   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   13  S   UNK     0      -4.001   3.850   0.000  0.00  0.00           S+0
CONECT    1   13                                                            
CONECT    2    4    5                                                       
CONECT    3    6    7                                                       
CONECT    4    2    8                                                       
CONECT    5    2    9                                                       
CONECT    6    3   10                                                       
CONECT    7    3   11                                                       
CONECT    8    4   12                                                       
CONECT    9    5   12                                                       
CONECT   10    6   12                                                       
CONECT   11    7   13                                                       
CONECT   12    8    9   10                                                  
CONECT   13    1   11                                                       
MASTER        0    0    0    0    0    0    0    0   13    0   26    0
END

View in JSmol View Stereo Labels

Synonyms

Value	Source
[(4Z)-5-(Methylsulphanyl)pent-4-en-2-yn-1-yl]benzene	HMDB

Chemical Formula

C₁₂H₁₂S

Average Molecular Weight

188.289

Monoisotopic Molecular Weight

188.065971074

IUPAC Name

[(4Z)-5-(methylsulfanyl)pent-4-en-2-yn-1-yl]benzene

Traditional Name

[(4Z)-5-(methylsulfanyl)pent-4-en-2-yn-1-yl]benzene

CAS Registry Number

Not Available

SMILES

CS\C=C/C#CCC1=CC=CC=C1

InChI Identifier

InChI=1S/C12H12S/c1-13-11-7-3-6-10-12-8-4-2-5-9-12/h2,4-5,7-9,11H,10H2,1H3/b11-7-

InChI Key

BQJDNQQWNLQSGB-XFFZJAGNSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as benzene and substituted derivatives. These are aromatic compounds containing one monocyclic ring system consisting of benzene.

Kingdom

Organic compounds

Super Class

Benzenoids

Class

Benzene and substituted derivatives

Sub Class

Not Available

Direct Parent

Benzene and substituted derivatives

Alternative Parents

Substituents

Monocyclic benzene moiety
Thioenolether
Sulfenyl compound
Hydrocarbon derivative
Organosulfur compound
Aromatic homomonocyclic compound

Molecular Framework

Aromatic homomonocyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Membrane (HMDB: HMDB0032688)
Cell membrane (HMDB: HMDB0032688)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0032688)

Source

Endogenous

Endogenous (HMDB: HMDB0032688)

Plant

Plant (HMDB: HMDB0032688)

Exogenous

Food

Food (HMDB: HMDB0032688)

Herb and spice

Herbs and Spices (FooDB: FOOD00866)

Exogenous (HMDB: HMDB0032688)

Process

Not Available

Role

Not Available

Physical Properties

State

Not Available

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	0.0069 g/L	ALOGPS
logP	4.09	ALOGPS
logP	3.78	ChemAxon
logS	-4.4	ALOGPS
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	0	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	0 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	61.76 m³·mol⁻¹	ChemAxon
Polarizability	21.15 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	145.267	31661259
DarkChem	[M-H]-	140.084	31661259
DeepCCS	[M+H]+	138.065	30932474
DeepCCS	[M-H]-	134.712	30932474
DeepCCS	[M-2H]-	171.8	30932474
DeepCCS	[M+Na]+	147.338	30932474
AllCCS	[M+H]+	139.0	32859911
AllCCS	[M+H-H2O]+	134.8	32859911
AllCCS	[M+NH4]+	142.9	32859911
AllCCS	[M+Na]+	144.1	32859911
AllCCS	[M-H]-	143.1	32859911
AllCCS	[M+Na-2H]-	143.7	32859911
AllCCS	[M+HCOO]-	144.5	32859911

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
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.	8.53 minutes	32390414
Predicted by Siyang on May 30, 2022	17.0465 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	1.8 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	2323.4 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	609.1 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	232.7 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	407.4 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	371.0 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	769.9 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	679.2 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	136.0 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	1536.7 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	576.8 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	1470.9 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	506.4 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	431.5 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	517.8 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	470.6 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	24.2 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
(Z)-1-(Methylthio)-5-phenyl-1-penten-3-yne	CS\C=C/C#CCC1=CC=CC=C1	2341.0	Standard polar	33892256
(Z)-1-(Methylthio)-5-phenyl-1-penten-3-yne	CS\C=C/C#CCC1=CC=CC=C1	1709.7	Standard non polar	33892256
(Z)-1-(Methylthio)-5-phenyl-1-penten-3-yne	CS\C=C/C#CCC1=CC=CC=C1	1705.9	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - (Z)-1-(Methylthio)-5-phenyl-1-penten-3-yne GC-MS (Non-derivatized) - 70eV, Positive	splash10-0006-9800000000-75a2e26c4edff513e14e	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (Z)-1-(Methylthio)-5-phenyl-1-penten-3-yne GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (Z)-1-(Methylthio)-5-phenyl-1-penten-3-yne 10V, Positive-QTOF	splash10-000i-1900000000-85b96d6a8bade468ed7e	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (Z)-1-(Methylthio)-5-phenyl-1-penten-3-yne 20V, Positive-QTOF	splash10-000f-4900000000-a705ff403fbf497b18a4	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (Z)-1-(Methylthio)-5-phenyl-1-penten-3-yne 40V, Positive-QTOF	splash10-0006-9300000000-3282a9d72da111e07d43	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (Z)-1-(Methylthio)-5-phenyl-1-penten-3-yne 10V, Negative-QTOF	splash10-000j-6900000000-6e7a6498303d22d22aff	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (Z)-1-(Methylthio)-5-phenyl-1-penten-3-yne 20V, Negative-QTOF	splash10-0002-9200000000-1d004706b8947bd20df8	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (Z)-1-(Methylthio)-5-phenyl-1-penten-3-yne 40V, Negative-QTOF	splash10-0002-9000000000-29cd727c15c88be80607	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (Z)-1-(Methylthio)-5-phenyl-1-penten-3-yne 10V, Positive-QTOF	splash10-000f-5900000000-17fd053a63355aa40f3b	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (Z)-1-(Methylthio)-5-phenyl-1-penten-3-yne 20V, Positive-QTOF	splash10-00kf-7900000000-c6ef2c1068ab4ce64ec7	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (Z)-1-(Methylthio)-5-phenyl-1-penten-3-yne 40V, Positive-QTOF	splash10-002f-9400000000-6b99a08a149405529662	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (Z)-1-(Methylthio)-5-phenyl-1-penten-3-yne 10V, Negative-QTOF	splash10-000i-0900000000-c2f34d76e9e4e25c0288	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (Z)-1-(Methylthio)-5-phenyl-1-penten-3-yne 20V, Negative-QTOF	splash10-000i-6900000000-9f345159c3ee19782029	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (Z)-1-(Methylthio)-5-phenyl-1-penten-3-yne 40V, Negative-QTOF	splash10-00mx-9600000000-c28dd466297f4f02ba9f	2021-09-25	Wishart Lab	View Spectrum

IR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)	2023-02-04	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)	2023-02-04	FELIX lab	View Spectrum

Biological Properties

Cellular Locations

Membrane

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB010645

KNApSAcK ID

Not Available

Chemspider ID

30776947

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

131751283

PDB ID

Not Available

ChEBI ID

173894

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

(). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .

Showing metabocard for (Z)-1-(Methylthio)-5-phenyl-1-penten-3-yne (HMDB0032688)

MOL for HMDB0032688 ((Z)-1-(Methylthio)-5-phenyl-1-penten-3-yne)

3D MOL for HMDB0032688 ((Z)-1-(Methylthio)-5-phenyl-1-penten-3-yne)

3D SDF for HMDB0032688 ((Z)-1-(Methylthio)-5-phenyl-1-penten-3-yne)

3D-SDF for HMDB0032688 ((Z)-1-(Methylthio)-5-phenyl-1-penten-3-yne)

PDB for HMDB0032688 ((Z)-1-(Methylthio)-5-phenyl-1-penten-3-yne)

3D PDB for HMDB0032688 ((Z)-1-(Methylthio)-5-phenyl-1-penten-3-yne)

SMILES for HMDB0032688 ((Z)-1-(Methylthio)-5-phenyl-1-penten-3-yne)

INCHI for HMDB0032688 ((Z)-1-(Methylthio)-5-phenyl-1-penten-3-yne)

Structure for HMDB0032688 ((Z)-1-(Methylthio)-5-phenyl-1-penten-3-yne)

3D Structure for HMDB0032688 ((Z)-1-(Methylthio)-5-phenyl-1-penten-3-yne)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra

IR Spectra