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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-10 21:25:34 UTC

Update Date

2021-09-26 22:51:53 UTC

HMDB ID

HMDB0244254

Secondary Accession Numbers

None

Metabolite Identification

Common Name

1,9-Decadiene

Description

1,9-Decadiene, also known as deca-19-diene, belongs to the class of organic compounds known as alkadienes. These are acyclic hydrocarbons that contain exactly two carbon-to-carbon double bonds. Based on a literature review a significant number of articles have been published on 1,9-Decadiene. This compound has been identified in human blood as reported by (PMID: 31557052 ). 1,9-decadiene is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 1,9-Decadiene is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.

Structure

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

COMPND    HMDB0244254
HETATM    1  C1  UNL     1       3.697  -0.150  -1.106  1.00  0.00           C  
HETATM    2  C2  UNL     1       3.351  -0.339   0.144  1.00  0.00           C  
HETATM    3  C3  UNL     1       2.207   0.401   0.734  1.00  0.00           C  
HETATM    4  C4  UNL     1       1.149  -0.546   1.216  1.00  0.00           C  
HETATM    5  C5  UNL     1       0.636  -1.390   0.087  1.00  0.00           C  
HETATM    6  C6  UNL     1       0.045  -0.548  -0.987  1.00  0.00           C  
HETATM    7  C7  UNL     1      -1.104   0.288  -0.503  1.00  0.00           C  
HETATM    8  C8  UNL     1      -2.236  -0.516   0.053  1.00  0.00           C  
HETATM    9  C9  UNL     1      -3.295   0.437   0.489  1.00  0.00           C  
HETATM   10  C10 UNL     1      -4.506   0.390  -0.039  1.00  0.00           C  
HETATM   11  H1  UNL     1       4.539  -0.701  -1.524  1.00  0.00           H  
HETATM   12  H2  UNL     1       3.186   0.531  -1.750  1.00  0.00           H  
HETATM   13  H3  UNL     1       3.892  -1.039   0.776  1.00  0.00           H  
HETATM   14  H4  UNL     1       2.590   1.008   1.607  1.00  0.00           H  
HETATM   15  H5  UNL     1       1.827   1.148   0.020  1.00  0.00           H  
HETATM   16  H6  UNL     1       1.533  -1.184   2.063  1.00  0.00           H  
HETATM   17  H7  UNL     1       0.330   0.050   1.701  1.00  0.00           H  
HETATM   18  H8  UNL     1      -0.091  -2.118   0.511  1.00  0.00           H  
HETATM   19  H9  UNL     1       1.491  -2.009  -0.262  1.00  0.00           H  
HETATM   20  H10 UNL     1      -0.242  -1.181  -1.864  1.00  0.00           H  
HETATM   21  H11 UNL     1       0.821   0.136  -1.386  1.00  0.00           H  
HETATM   22  H12 UNL     1      -1.492   0.942  -1.315  1.00  0.00           H  
HETATM   23  H13 UNL     1      -0.741   0.979   0.272  1.00  0.00           H  
HETATM   24  H14 UNL     1      -2.631  -1.262  -0.662  1.00  0.00           H  
HETATM   25  H15 UNL     1      -1.912  -1.049   0.992  1.00  0.00           H  
HETATM   26  H16 UNL     1      -3.069   1.175   1.246  1.00  0.00           H  
HETATM   27  H17 UNL     1      -5.269   1.081   0.280  1.00  0.00           H  
HETATM   28  H18 UNL     1      -4.704  -0.359  -0.794  1.00  0.00           H  
CONECT    1    2    2   11   12
CONECT    2    3   13
CONECT    3    4   14   15
CONECT    4    5   16   17
CONECT    5    6   18   19
CONECT    6    7   20   21
CONECT    7    8   22   23
CONECT    8    9   24   25
CONECT    9   10   10   26
CONECT   10   27   28
END

View in JSmol View Stereo Labels

Synonyms

Value	Source
Deca-19-diene	HMDB
1,9-Decadiene	MeSH

Chemical Formula

C₁₀H₁₈

Average Molecular Weight

138.254

Monoisotopic Molecular Weight

138.14085058

IUPAC Name

deca-1,9-diene

Traditional Name

1,9-decadiene

CAS Registry Number

Not Available

SMILES

C=CCCCCCCC=C

InChI Identifier

InChI=1S/C10H18/c1-3-5-7-9-10-8-6-4-2/h3-4H,1-2,5-10H2

InChI Key

NLDGJRWPPOSWLC-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as alkadienes. These are acyclic hydrocarbons that contain exactly two carbon-to-carbon double bonds.

Kingdom

Organic compounds

Super Class

Hydrocarbons

Class

Unsaturated hydrocarbons

Sub Class

Olefins

Direct Parent

Alkadienes

Alternative Parents

Unsaturated aliphatic hydrocarbons

Substituents

Alkadiene
Unsaturated aliphatic hydrocarbon
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 31557052)

Source

Exogenous

Exogenous (PMID: 31557052)

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
logP	5.03	ALOGPS
logP	4.3	ChemAxon
logS	-4.6	ALOGPS
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	0	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	0 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	47.9 m³·mol⁻¹	ChemAxon
Polarizability	18.72 Å³	ChemAxon
Number of Rings	0	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]+	142.974	30932474
DeepCCS	[M-H]-	140.616	30932474
DeepCCS	[M-2H]-	176.331	30932474
DeepCCS	[M+Na]+	151.521	30932474
AllCCS	[M+H]+	137.4	32859911
AllCCS	[M+H-H2O]+	133.2	32859911
AllCCS	[M+NH4]+	141.3	32859911
AllCCS	[M+Na]+	142.4	32859911
AllCCS	[M-H]-	139.4	32859911
AllCCS	[M+Na-2H]-	141.7	32859911
AllCCS	[M+HCOO]-	144.3	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.	7.55 minutes	32390414
Predicted by Siyang on May 30, 2022	18.9879 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	5.01 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	2342.0 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	662.1 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	251.0 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	471.5 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	430.5 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	767.0 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	869.1 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	184.7 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	1735.2 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	534.2 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	1589.2 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	613.5 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	498.9 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	691.9 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	592.2 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	10.5 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
1,9-Decadiene	C=CCCCCCCC=C	1122.6	Standard polar	33892256
1,9-Decadiene	C=CCCCCCCC=C	967.2	Standard non polar	33892256
1,9-Decadiene	C=CCCCCCCC=C	958.1	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 - 1,9-Decadiene GC-MS (Non-derivatized) - 70eV, Positive	splash10-05p6-9100000000-43f7b0fd4acddc7e50e1	2021-09-24	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 1,9-Decadiene 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 - 1,9-Decadiene 10V, Positive-QTOF	splash10-000i-0900000000-4d5d811b56ed55f265bc	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1,9-Decadiene 20V, Positive-QTOF	splash10-000i-6900000000-ef856228a7c3d3bc05d7	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1,9-Decadiene 40V, Positive-QTOF	splash10-0k96-9000000000-396851bba6a2faca9900	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1,9-Decadiene 10V, Negative-QTOF	splash10-000i-0900000000-d449c55611d192409c3a	2016-08-04	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1,9-Decadiene 20V, Negative-QTOF	splash10-000i-0900000000-baa106a8f474c7a14fe1	2016-08-04	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1,9-Decadiene 40V, Negative-QTOF	splash10-000i-9500000000-d7c57de5d5d3d617fcd0	2016-08-04	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1,9-Decadiene 10V, Positive-QTOF	splash10-067i-9000000000-4da13a6a326dfc19a8ed	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1,9-Decadiene 20V, Positive-QTOF	splash10-066r-9000000000-94fde26871a7c927e39f	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1,9-Decadiene 40V, Positive-QTOF	splash10-0aou-9000000000-dba5a7e3ac10b496307b	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1,9-Decadiene 10V, Negative-QTOF	splash10-000i-0900000000-005b492eed114057487d	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1,9-Decadiene 20V, Negative-QTOF	splash10-000i-0900000000-0ffa5a228e1bbc16c17a	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1,9-Decadiene 40V, Negative-QTOF	splash10-014i-9000000000-0a1a402ea6b86d9d0c3b	2021-10-12	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	31557052	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

14692

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

15439

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

Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]

Showing metabocard for 1,9-Decadiene (HMDB0244254)

MOL for HMDB0244254 (1,9-Decadiene)

3D MOL for HMDB0244254 (1,9-Decadiene)

3D SDF for HMDB0244254 (1,9-Decadiene)

3D-SDF for HMDB0244254 (1,9-Decadiene)

PDB for HMDB0244254 (1,9-Decadiene)

3D PDB for HMDB0244254 (1,9-Decadiene)

SMILES for HMDB0244254 (1,9-Decadiene)

INCHI for HMDB0244254 (1,9-Decadiene)

Structure for HMDB0244254 (1,9-Decadiene)

3D Structure for HMDB0244254 (1,9-Decadiene)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra