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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2014-10-08 15:56:52 UTC

Update Date

2022-03-07 03:17:49 UTC

HMDB ID

HMDB0061897

Secondary Accession Numbers

HMDB61897

Metabolite Identification

Common Name

(Z)-1,3-Octadiene

Description

(Z)-1,3-Octadiene belongs to the class of organic compounds known as cycloalkenes. These are compounds containing a non-aromatic closed ring of carbon atoms in which at least 2 atoms are connected by a double bond.

Structure

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

HEADER    PROTEIN                                 08-OCT-14   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   08-OCT-14         0                                  
HETATM    1  C   UNK     0       3.195   2.366   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.803   3.025   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       3.713   0.916   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.144   1.633   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.055  -0.476   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.306   1.114   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.605  -0.994   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.213  -0.336   0.000  0.00  0.00           C+0
HETATM    9  H   UNK     0       4.336   3.400   0.000  0.00  0.00           H+0
HETATM   10  H   UNK     0       1.284   4.475   0.000  0.00  0.00           H+0
HETATM   11  H   UNK     0       5.251   0.841   0.000  0.00  0.00           H+0
HETATM   12  H   UNK     0       2.178   0.492   0.000  0.00  0.00           H+0
CONECT    1    2    3    9                                                  
CONECT    2    1    4   10                                                  
CONECT    3    1    5   11                                                  
CONECT    4    2    6   12                                                  
CONECT    5    3    7                                                       
CONECT    6    4    8                                                       
CONECT    7    5    8                                                       
CONECT    8    6    7                                                       
CONECT    9    1                                                            
CONECT   10    2                                                            
CONECT   11    3                                                            
CONECT   12    4                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   24    0
END

View in JSmol View Stereo Labels

Synonyms

Not Available

Chemical Formula

C₈H₁₂

Average Molecular Weight

108.1809

Monoisotopic Molecular Weight

108.093900384

IUPAC Name

(1Z,3E)-cycloocta-1,3-diene

Traditional Name

(1Z,3E)-cycloocta-1,3-diene

CAS Registry Number

Not Available

SMILES

[H]\C1=C(\[H])/C(/[H])=C([H])\CCCC1

InChI Identifier

InChI=1S/C8H12/c1-2-4-6-8-7-5-3-1/h1-4H,5-8H2/b3-1-,4-2+

InChI Key

RRKODOZNUZCUBN-HSFFGMMNSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as cycloalkenes. These are unsaturated monocyclic hydrocarbons having one endocyclic double bond.

Kingdom

Organic compounds

Super Class

Hydrocarbons

Class

Unsaturated hydrocarbons

Sub Class

Olefins

Direct Parent

Cycloalkenes

Alternative Parents

Unsaturated aliphatic hydrocarbons

Substituents

Cycloalkene
Unsaturated aliphatic hydrocarbon
Aliphatic homomonocyclic compound

Molecular Framework

Aliphatic homomonocyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Saliva (PMID: 24421258)

Source

Exogenous

Exogenous (HMDB: HMDB0061897)

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	0.048 g/L	ALOGPS
logP	3.56	ALOGPS
logP	2.83	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	0	ChemAxon
Refractivity	39.04 m³·mol⁻¹	ChemAxon
Polarizability	13.2 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
DeepCCS	[M+H]+	134.232	30932474
DeepCCS	[M-H]-	132.011	30932474
DeepCCS	[M-2H]-	166.018	30932474
DeepCCS	[M+Na]+	140.223	30932474
AllCCS	[M+H]+	123.9	32859911
AllCCS	[M+H-H2O]+	119.2	32859911
AllCCS	[M+NH4]+	128.4	32859911
AllCCS	[M+Na]+	129.7	32859911
AllCCS	[M-H]-	124.7	32859911
AllCCS	[M+Na-2H]-	127.3	32859911
AllCCS	[M+HCOO]-	130.2	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 √ó 2.1 mm; 1.7 Œºmparticle diameter). Predicted by Afia on May 17, 2022.	3.99 minutes	32390414
Predicted by Siyang on May 30, 2022	18.4096 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	5.96 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	2094.7 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	633.7 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	266.6 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	506.2 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	426.0 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	711.6 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	519.0 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	168.4 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	1623.3 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	531.8 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	1266.1 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	620.8 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	490.7 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	619.3 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	591.3 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	68.0 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
(Z)-1,3-Octadiene	[H]\C1=C(\[H])/C(/[H])=C([H])\CCCC1	1734.2	Standard polar	33892256
(Z)-1,3-Octadiene	[H]\C1=C(\[H])/C(/[H])=C([H])\CCCC1	918.9	Standard non polar	33892256
(Z)-1,3-Octadiene	[H]\C1=C(\[H])/C(/[H])=C([H])\CCCC1	978.8	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)-1,3-Octadiene GC-MS (Non-derivatized) - 70eV, Positive	splash10-0a4i-9500000000-30432475a3f1d3b43bfb	2017-09-20	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (Z)-1,3-Octadiene GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (Z)-1,3-Octadiene 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)-1,3-Octadiene 10V, Positive-QTOF	splash10-0a4i-0900000000-94853c333389cb7a9941	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (Z)-1,3-Octadiene 20V, Positive-QTOF	splash10-0a4i-1900000000-c7ea70bfdf6955cbd8c0	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (Z)-1,3-Octadiene 40V, Positive-QTOF	splash10-0udl-9000000000-d8f4784c0025fb2e4f39	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (Z)-1,3-Octadiene 10V, Negative-QTOF	splash10-0a4i-0900000000-b586e07f6905aef9e541	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (Z)-1,3-Octadiene 20V, Negative-QTOF	splash10-0a4i-0900000000-b8aa7cbc15e998d1ae85	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (Z)-1,3-Octadiene 40V, Negative-QTOF	splash10-0a6r-9500000000-a875e6a166b22a9b9af6	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (Z)-1,3-Octadiene 10V, Positive-QTOF	splash10-0a4i-2900000000-da91c7ad60b1d3b319c7	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (Z)-1,3-Octadiene 20V, Positive-QTOF	splash10-0a4i-9400000000-e1afc449d142859debe8	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (Z)-1,3-Octadiene 40V, Positive-QTOF	splash10-0ar3-9000000000-59f23540e8d76bb63a02	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (Z)-1,3-Octadiene 10V, Negative-QTOF	splash10-0a4i-0900000000-e16413f7e638bb43ede9	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (Z)-1,3-Octadiene 20V, Negative-QTOF	splash10-0a4i-0900000000-e16413f7e638bb43ede9	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (Z)-1,3-Octadiene 40V, Negative-QTOF	splash10-0a4i-5900000000-844c732e0ae393c33fc6	2021-09-25	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Saliva

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Saliva	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Not Specified	Normal	24421258	details

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

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

6432393

PDB ID

Not Available

ChEBI ID

88407

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

Baldwin JE, Burrell RC: Kinetics of thermal gas-phase isomerizations and fragmentations of cis- and trans-1-(E)-propenyl-2-methylcyclobutanes at 275 degrees C. J Org Chem. 2002 May 17;67(10):3249-56. [PubMed:12003532 ]

Showing metabocard for (Z)-1,3-Octadiene (HMDB0061897)

MOL for HMDB0061897 ((Z)-1,3-Octadiene)

3D MOL for HMDB0061897 ((Z)-1,3-Octadiene)

3D SDF for HMDB0061897 ((Z)-1,3-Octadiene)

3D-SDF for HMDB0061897 ((Z)-1,3-Octadiene)

PDB for HMDB0061897 ((Z)-1,3-Octadiene)

3D PDB for HMDB0061897 ((Z)-1,3-Octadiene)

SMILES for HMDB0061897 ((Z)-1,3-Octadiene)

INCHI for HMDB0061897 ((Z)-1,3-Octadiene)

Structure for HMDB0061897 ((Z)-1,3-Octadiene)

3D Structure for HMDB0061897 ((Z)-1,3-Octadiene)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra