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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2013-03-07 21:32:04 UTC

Update Date

2022-03-07 03:17:36 UTC

HMDB ID

HMDB0059834

Secondary Accession Numbers

HMDB59834

Metabolite Identification

Common Name

Pentylbenzene

Description

Pentylbenzene 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. Pentylbenzene can be found in lovage and wild celery, which makes pentylbenzene a potential biomarker for the consumption of these food products. Pentylbenzene is possibly neutral. Outside of the human body, Pentylbenzene is found, on average, in the highest concentration within wild celeries. Pentylbenzene has also been detected, but not quantified in, a few different foods, such as celeriacs, celery stalks, and lovages. This could make pentylbenzene a potential biomarker for the consumption of these foods. Pentylbenzene exists in all eukaryotes, ranging from yeast to humans. Pentylbenzene belongs to benzene and substituted derivatives class of compounds. Those are aromatic compounds containing one monocyclic ring system consisting of benzene. These are aromatic compounds containing a benzene substituted at one or more positions.

Structure

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

COMPND    HMDB0059834
HETATM    1  C1  UNL     1      -3.156   0.392  -0.550  1.00  0.00           C  
HETATM    2  C2  UNL     1      -3.076  -0.521   0.622  1.00  0.00           C  
HETATM    3  C3  UNL     1      -1.980  -0.183   1.548  1.00  0.00           C  
HETATM    4  C4  UNL     1      -0.620  -0.311   1.025  1.00  0.00           C  
HETATM    5  C5  UNL     1      -0.168   0.472  -0.141  1.00  0.00           C  
HETATM    6  C6  UNL     1       1.301   0.147  -0.383  1.00  0.00           C  
HETATM    7  C7  UNL     1       1.645  -0.884  -1.207  1.00  0.00           C  
HETATM    8  C8  UNL     1       2.968  -1.224  -1.462  1.00  0.00           C  
HETATM    9  C9  UNL     1       3.929  -0.453  -0.829  1.00  0.00           C  
HETATM   10  C10 UNL     1       3.594   0.589   0.004  1.00  0.00           C  
HETATM   11  C11 UNL     1       2.272   0.893   0.231  1.00  0.00           C  
HETATM   12  H1  UNL     1      -4.243   0.710  -0.663  1.00  0.00           H  
HETATM   13  H2  UNL     1      -2.574   1.329  -0.475  1.00  0.00           H  
HETATM   14  H3  UNL     1      -2.917  -0.082  -1.522  1.00  0.00           H  
HETATM   15  H4  UNL     1      -2.950  -1.579   0.213  1.00  0.00           H  
HETATM   16  H5  UNL     1      -4.078  -0.594   1.161  1.00  0.00           H  
HETATM   17  H6  UNL     1      -2.195   0.836   1.984  1.00  0.00           H  
HETATM   18  H7  UNL     1      -2.101  -0.878   2.447  1.00  0.00           H  
HETATM   19  H8  UNL     1       0.122  -0.078   1.864  1.00  0.00           H  
HETATM   20  H9  UNL     1      -0.384  -1.406   0.791  1.00  0.00           H  
HETATM   21  H10 UNL     1      -0.244   1.566  -0.045  1.00  0.00           H  
HETATM   22  H11 UNL     1      -0.681   0.185  -1.109  1.00  0.00           H  
HETATM   23  H12 UNL     1       0.898  -1.510  -1.720  1.00  0.00           H  
HETATM   24  H13 UNL     1       3.244  -2.041  -2.114  1.00  0.00           H  
HETATM   25  H14 UNL     1       4.966  -0.715  -1.026  1.00  0.00           H  
HETATM   26  H15 UNL     1       4.406   1.141   0.459  1.00  0.00           H  
HETATM   27  H16 UNL     1       2.022   1.727   0.897  1.00  0.00           H  
CONECT    1    2   12   13   14
CONECT    2    3   15   16
CONECT    3    4   17   18
CONECT    4    5   19   20
CONECT    5    6   21   22
CONECT    6    7    7   11
CONECT    7    8   23
CONECT    8    9    9   24
CONECT    9   10   25
CONECT   10   11   11   26
CONECT   11   27
END

View in JSmol View Stereo Labels

Synonyms

Value	Source
N-Amylbenzene	HMDB

Chemical Formula

C₁₁H₁₆

Average Molecular Weight

148.2447

Monoisotopic Molecular Weight

148.125200512

IUPAC Name

pentylbenzene

Traditional Name

pentylbenzene

CAS Registry Number

Not Available

SMILES

CCCCCC1=CC=CC=C1

InChI Identifier

InChI=1S/C11H16/c1-2-3-5-8-11-9-6-4-7-10-11/h4,6-7,9-10H,2-3,5,8H2,1H3

InChI Key

PWATWSYOIIXYMA-UHFFFAOYSA-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
Aromatic hydrocarbon
Unsaturated hydrocarbon
Hydrocarbon
Aromatic homomonocyclic compound

Molecular Framework

Aromatic homomonocyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Membrane (HMDB: HMDB0059834)
Cell membrane (HMDB: HMDB0059834)

Source

Exogenous

Exogenous (HMDB: HMDB0059834)

Food

Vegetable

Root vegetable

Celeriac (FooDB: FOOD00214)

Stalk vegetable

Celery stalks (FooDB: FOOD00215)

Herb and spice

Spice

Wild celery (FooDB: FOOD00015)

Herb

Lovage (FooDB: FOOD00100)

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	0.0024 g/L	ALOGPS
logP	4.81	ALOGPS
logP	4.26	ChemAxon
logS	-4.8	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	49.5 m³·mol⁻¹	ChemAxon
Polarizability	19.1 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]+	134.04	31661259
DarkChem	[M-H]-	131.225	31661259
DeepCCS	[M+H]+	137.04	30932474
DeepCCS	[M-H]-	133.524	30932474
DeepCCS	[M-2H]-	170.961	30932474
DeepCCS	[M+Na]+	146.243	30932474
AllCCS	[M+H]+	133.2	32859911
AllCCS	[M+H-H2O]+	128.6	32859911
AllCCS	[M+NH4]+	137.4	32859911
AllCCS	[M+Na]+	138.6	32859911
AllCCS	[M-H]-	139.6	32859911
AllCCS	[M+Na-2H]-	141.1	32859911
AllCCS	[M+HCOO]-	142.7	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.	8.37 minutes	32390414
Predicted by Siyang on May 30, 2022	19.4393 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	3.9 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	2503.5 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	735.7 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	283.1 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	498.4 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	418.9 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	865.1 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	886.4 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	293.4 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	1756.8 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	660.3 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	1720.3 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	598.9 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	532.7 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	642.8 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	534.9 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	16.7 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Pentylbenzene	CCCCCC1=CC=CC=C1	1419.6	Standard polar	33892256
Pentylbenzene	CCCCCC1=CC=CC=C1	1150.5	Standard non polar	33892256
Pentylbenzene	CCCCCC1=CC=CC=C1	1148.1	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Experimental GC-MS	GC-MS Spectrum - Pentylbenzene EI-B (Non-derivatized)	splash10-0006-9100000000-2d0366b3b374b5ee38c0	2017-09-12	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - Pentylbenzene CI-B (Non-derivatized)	splash10-006t-5900000000-9b44dd941f1ca9387f81	2017-09-12	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - Pentylbenzene EI-B (Non-derivatized)	splash10-0006-9100000000-2d0366b3b374b5ee38c0	2018-05-18	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - Pentylbenzene CI-B (Non-derivatized)	splash10-006t-5900000000-9b44dd941f1ca9387f81	2018-05-18	HMDB team, MONA, MassBank	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Pentylbenzene GC-MS (Non-derivatized) - 70eV, Positive	splash10-0006-9400000000-7be2a557c97883139a59	2016-09-22	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Pentylbenzene 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 - Pentylbenzene 10V, Positive-QTOF	splash10-0002-1900000000-b772868af56564b0b2bf	2015-04-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pentylbenzene 20V, Positive-QTOF	splash10-0002-8900000000-fb933e4cea868a07ca92	2015-04-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pentylbenzene 40V, Positive-QTOF	splash10-0a4l-9100000000-f6a8b92ad7802bb82e37	2015-04-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pentylbenzene 10V, Negative-QTOF	splash10-0002-0900000000-7ef302817cbd9a07af4d	2015-04-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pentylbenzene 20V, Negative-QTOF	splash10-0002-0900000000-29d568de75d058e5eb86	2015-04-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pentylbenzene 40V, Negative-QTOF	splash10-0035-8900000000-16d67043dddfe8c1f733	2015-04-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pentylbenzene 10V, Negative-QTOF	splash10-0002-0900000000-ab1ae225efa93f5b6fa0	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pentylbenzene 20V, Negative-QTOF	splash10-0002-0900000000-ab1ae225efa93f5b6fa0	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pentylbenzene 40V, Negative-QTOF	splash10-002f-9000000000-e60b78bd4f6b35d4f2e4	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pentylbenzene 10V, Positive-QTOF	splash10-0006-9300000000-6dfadd277e3743957639	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pentylbenzene 20V, Positive-QTOF	splash10-052f-9100000000-c263b1aaaccef83c675b	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pentylbenzene 40V, Positive-QTOF	splash10-0006-9300000000-9be05898b72b11531a13	2021-09-24	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Membrane (predicted from logP)

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

FDB003965

KNApSAcK ID

Not Available

Chemspider ID

10404

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

10864

PDB ID

Not Available

ChEBI ID

Not Available

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

Not Available

Showing metabocard for Pentylbenzene (HMDB0059834)

MOL for HMDB0059834 (Pentylbenzene)

3D MOL for HMDB0059834 (Pentylbenzene)

3D SDF for HMDB0059834 (Pentylbenzene)

3D-SDF for HMDB0059834 (Pentylbenzene)

PDB for HMDB0059834 (Pentylbenzene)

3D PDB for HMDB0059834 (Pentylbenzene)

SMILES for HMDB0059834 (Pentylbenzene)

INCHI for HMDB0059834 (Pentylbenzene)

Structure for HMDB0059834 (Pentylbenzene)

3D Structure for HMDB0059834 (Pentylbenzene)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra