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Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References XML

Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2012-09-12 01:46:34 UTC

Update Date

2023-02-21 17:28:01 UTC

HMDB ID

HMDB0040240

Secondary Accession Numbers

HMDB40240

Metabolite Identification

Common Name

2-Pentylthiophene

Description

2-Pentylthiophene is a member of thiophenes. 2-Pentylthiophene belongs to the class of organic compounds known as heteroaromatic compounds. Heteroaromatic compounds are compounds containing an aromatic ring where a carbon atom is linked to an hetero atom. 2-Pentylthiophene is possibly neutral. 2-Pentylthiophene is a sweet, cranberry, and fatty tasting compound. 2-Pentylthiophene has been detected, but not quantified, in herbs and spices and mushrooms. 2-Pentylthiophene has been found to be associated with several diseases such as pervasive developmental disorder not otherwise specified and autism in humans. 2-pentylthiophene has also been linked to the inborn metabolic disorder celiac disease.

Structure

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

View in JSmol View Stereo Labels

Synonyms

Value	Source
1-Methylbutylthiophene	HMDB
2-N-Amylthiophene	HMDB
2-N-Pentylthiophene	HMDB
2-Pentyl-thiophene	HMDB

Chemical Formula

C₉H₁₄S

Average Molecular Weight

154.272

Monoisotopic Molecular Weight

154.081621138

IUPAC Name

2-pentylthiophene

Traditional Name

2-pentylthiophene

CAS Registry Number

4861-58-9

SMILES

CCCCCC1=CC=CS1

InChI Identifier

InChI=1S/C9H14S/c1-2-3-4-6-9-7-5-8-10-9/h5,7-8H,2-4,6H2,1H3

InChI Key

NOYVOSGVFSEKPR-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as heteroaromatic compounds. Heteroaromatic compounds are compounds containing an aromatic ring where a carbon atom is linked to an hetero atom.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Heteroaromatic compounds

Sub Class

Not Available

Direct Parent

Heteroaromatic compounds

Alternative Parents

Substituents

Heteroaromatic compound
Thiophene
Hydrocarbon derivative
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Organoleptic effect

Taste

Sweet

Odor

Disposition

Biological location

Cellular substructure

Membrane (HMDB: HMDB0040240)
Cell membrane (HMDB: HMDB0040240)

Non-excretory biofluid

Biofluid or Excreta

Saliva (PMID: 24657864)

Excreta

Biofluid or Excreta

Feces (PMID: 24130822)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0040240)

Source

Exogenous

Exogenous (HMDB: HMDB0040240)

Food

Food (HMDB: HMDB0040240)

Vegetable

Mushroom

Herb and spice

Herbs and Spices (FooDB: FOOD00866)

Endogenous

Plant

Plant (HMDB: HMDB0040240)

Process

Not Available

Role

Biological role

Nutrient (HMDB: HMDB0040240)

Physical Properties

State

Not Available

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	96.00 °C. @ 30.00 mm Hg	The Good Scents Company Information System
Water Solubility	14.71 mg/L @ 25 °C (est)	The Good Scents Company Information System
LogP	4.282 (est)	The Good Scents Company Information System

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	0.057 g/L	ALOGPS
logP	4.39	ALOGPS
logP	4.18	ChemAxon
logS	-3.4	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	46.55 m³·mol⁻¹	ChemAxon
Polarizability	18.76 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	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]+	133.314	31661259
DarkChem	[M-H]-	129.448	31661259
DeepCCS	[M+H]+	140.46	30932474
DeepCCS	[M-H]-	138.398	30932474
DeepCCS	[M-2H]-	174.079	30932474
DeepCCS	[M+Na]+	148.852	30932474
AllCCS	[M+H]+	132.5	32859911
AllCCS	[M+H-H2O]+	128.0	32859911
AllCCS	[M+NH4]+	136.6	32859911
AllCCS	[M+Na]+	137.8	32859911
AllCCS	[M-H]-	140.7	32859911
AllCCS	[M+Na-2H]-	142.5	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.	6.75 minutes	32390414
Predicted by Siyang on May 30, 2022	19.0078 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	2.52 minutes	32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid	47.4 seconds	40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	2221.5 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	722.4 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	282.4 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	510.9 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	410.6 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	788.3 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	767.9 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	446.3 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	1667.6 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	587.2 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	1681.0 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	592.1 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	492.8 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	660.1 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	565.4 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	27.6 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
2-Pentylthiophene	CCCCCC1=CC=CS1	1427.3	Standard polar	33892256
2-Pentylthiophene	CCCCCC1=CC=CS1	1136.9	Standard non polar	33892256
2-Pentylthiophene	CCCCCC1=CC=CS1	1180.1	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Experimental GC-MS	GC-MS Spectrum - 2-Pentylthiophene EI-B (Non-derivatized)	splash10-0002-9200000000-67b9e327bdc1a8ebc8c9	2017-09-12	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - 2-Pentylthiophene EI-B (Non-derivatized)	splash10-0002-9200000000-67b9e327bdc1a8ebc8c9	2018-05-18	HMDB team, MONA, MassBank	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-Pentylthiophene GC-MS (Non-derivatized) - 70eV, Positive	splash10-002e-9300000000-b12c7e1aa288b8952c92	2016-09-22	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-Pentylthiophene GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-Pentylthiophene 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 - 2-Pentylthiophene 10V, Positive-QTOF	splash10-0a4i-0900000000-1e4ed805ae22c7f413c4	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Pentylthiophene 20V, Positive-QTOF	splash10-0ab9-9800000000-85e720996ac9d5b89fcf	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Pentylthiophene 40V, Positive-QTOF	splash10-0006-9000000000-d40ca661bf5c3c99bbc8	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Pentylthiophene 10V, Negative-QTOF	splash10-0udi-0900000000-9ff2aa5516dd2a5e79ca	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Pentylthiophene 20V, Negative-QTOF	splash10-0udi-1900000000-f0518d5eac2a37ed32aa	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Pentylthiophene 40V, Negative-QTOF	splash10-0a4i-9100000000-67c664332091be641693	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Pentylthiophene 10V, Positive-QTOF	splash10-0btd-9700000000-f015f26343976aa6c397	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Pentylthiophene 20V, Positive-QTOF	splash10-052f-9200000000-a02c1f6c7b074c77c64a	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Pentylthiophene 40V, Positive-QTOF	splash10-014j-9000000000-63d55ba07042421cc8d9	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Pentylthiophene 10V, Negative-QTOF	splash10-0udi-0900000000-f7e6ff7e0074f1c4f824	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Pentylthiophene 20V, Negative-QTOF	splash10-0udi-2900000000-a4743750430997a8f389	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Pentylthiophene 40V, Negative-QTOF	splash10-001j-9100000000-7af7e0d3b68e75e3b80d	2021-09-25	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)	2022-08-17	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	2022-08-17	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	2022-08-17	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	2022-08-17	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)	2022-08-17	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	2022-08-17	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)	2022-08-17	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	2022-08-17	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)	2022-08-17	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	2022-08-17	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)	2022-08-17	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	2022-08-17	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)	2022-08-17	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	2022-08-17	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)	2022-08-17	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	2022-08-17	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)	2022-08-17	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	2022-08-17	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)	2022-08-17	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	2022-08-17	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

Feces
Saliva

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Feces	Detected but not Quantified	Not Quantified	Children (1-13 years old)	Both	Normal	24130822	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	24922509	details
Saliva	Detected but not Quantified	Not Quantified	Children (1-13 years old)	Both	Normal	24657864	details

Abnormal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Feces	Detected but not Quantified	Not Quantified	Children (1-13 years old)	Both	Autism	24130822	details
Feces	Detected but not Quantified	Not Quantified	Children (1-13 years old)	Both	Pervasive Developmental Disorder Not Otherwise Specified	24130822	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Immunoglobulin A nephropathy (IgAN) non progressor	24922509	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Immunoglobulin A nephropathy (IgAN) progressor	24922509	details
Saliva	Detected but not Quantified	Not Quantified	Children (1-13 years old)	Both	Celiac disease	24657864	details

Associated Disorders and Diseases

Disease References

Autism
De Angelis M, Piccolo M, Vannini L, Siragusa S, De Giacomo A, Serrazzanetti DI, Cristofori F, Guerzoni ME, Gobbetti M, Francavilla R: Fecal microbiota and metabolome of children with autism and pervasive developmental disorder not otherwise specified. PLoS One. 2013 Oct 9;8(10):e76993. doi: 10.1371/journal.pone.0076993. eCollection 2013. [PubMed:24130822 ]
Pervasive developmental disorder not otherwise specified
De Angelis M, Piccolo M, Vannini L, Siragusa S, De Giacomo A, Serrazzanetti DI, Cristofori F, Guerzoni ME, Gobbetti M, Francavilla R: Fecal microbiota and metabolome of children with autism and pervasive developmental disorder not otherwise specified. PLoS One. 2013 Oct 9;8(10):e76993. doi: 10.1371/journal.pone.0076993. eCollection 2013. [PubMed:24130822 ]
Celiac disease
Francavilla R, Ercolini D, Piccolo M, Vannini L, Siragusa S, De Filippis F, De Pasquale I, Di Cagno R, Di Toma M, Gozzi G, Serrazanetti DI, De Angelis M, Gobbetti M: Salivary microbiota and metabolome associated with celiac disease. Appl Environ Microbiol. 2014 Jun;80(11):3416-25. doi: 10.1128/AEM.00362-14. Epub 2014 Mar 21. [PubMed:24657864 ]

Associated OMIM IDs

209850 (Autism)
212750 (Celiac disease)

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB019955

KNApSAcK ID

Not Available

Chemspider ID

19749

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

20995

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1048891

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 2-Pentylthiophene (HMDB0040240)

MOL for HMDB0040240 (2-Pentylthiophene)

3D MOL for HMDB0040240 (2-Pentylthiophene)

3D SDF for HMDB0040240 (2-Pentylthiophene)

3D-SDF for HMDB0040240 (2-Pentylthiophene)

PDB for HMDB0040240 (2-Pentylthiophene)

3D PDB for HMDB0040240 (2-Pentylthiophene)

SMILES for HMDB0040240 (2-Pentylthiophene)

INCHI for HMDB0040240 (2-Pentylthiophene)

Structure for HMDB0040240 (2-Pentylthiophene)

3D Structure for HMDB0040240 (2-Pentylthiophene)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

IR Spectra