Hmdb loader

Showing metabocard for (R)-1-Octen-3-ol (HMDB0031299)

Jump To Section:
IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesXML
Show more...Show more...Show more...
Record Information
Version5.0
StatusDetected and Quantified
Creation Date2012-09-11 17:42:11 UTC
Update Date2023-02-21 17:20:18 UTC
HMDB IDHMDB0031299
Secondary Accession Numbers
  • HMDB31299
Metabolite Identification
Common Name(R)-1-Octen-3-ol
Description(R)-1-Octen-3-ol, also known as 1-vinylhexanol or 3-hydroxy-1-octene, belongs to the class of organic compounds known as fatty alcohols. These are aliphatic alcohols consisting of a chain of a least six carbon atoms. Thus, (R)-1-octen-3-ol is considered to be a fatty alcohol. Based on a literature review a significant number of articles have been published on (R)-1-Octen-3-ol.
Structure
Data?1677000018
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0031299 ((R)-1-Octen-3-ol)

  Mrv1652305261923502D          

  9  8  0  0  0  0            999 V2000
    0.6336   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6349   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3480   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9204   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7770   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4914   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2059   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2059    0.5230    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  4  2  2  0  0  0  0
  5  3  1  0  0  0  0
  6  5  1  0  0  0  0
  7  6  1  0  0  0  0
  8  4  1  0  0  0  0
  8  7  1  0  0  0  0
  9  8  1  0  0  0  0
M  END
Download

3D MOL for HMDB0031299 ((R)-1-Octen-3-ol)

HMDB0031299
     RDKit          3D
(R)-1-Octen-3-ol
 25 24  0  0  0  0  0  0  0  0999 V2000
    2.9757   -1.6460   -0.5812 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4617   -0.6847   -1.3390 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8345    0.4781   -0.6485 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5579    0.7787    0.4907 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4179    0.0146   -0.2216 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2735    1.1434    0.4836 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6167    0.8954    1.0135 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7217    0.5057    0.1237 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5413   -0.8070   -0.5791 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4532   -2.5319   -1.0082 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9554   -1.6150    0.5054 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5146   -0.7765   -2.4023 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7585    1.3032   -1.3699 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4888    0.4240    0.3633 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1442   -0.2343   -1.1725 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4749   -0.9164    0.3577 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4455    1.4651    1.3092 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2253    2.0115   -0.2306 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5159    0.1082    1.8353 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9365    1.8479    1.5483 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6954    0.4380    0.7083 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9542    1.2701   -0.6631 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3579   -0.6577   -1.6671 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8007   -1.4729   -0.1249 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5551   -1.3417   -0.5580 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  2  3  1  0
  3  4  1  0
  3  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  1 10  1  0
  1 11  1  0
  2 12  1  0
  3 13  1  0
  4 14  1  0
  5 15  1  0
  5 16  1  0
  6 17  1  0
  6 18  1  0
  7 19  1  0
  7 20  1  0
  8 21  1  0
  8 22  1  0
  9 23  1  0
  9 24  1  0
  9 25  1  0
M  END
Download

3D SDF for HMDB0031299 ((R)-1-Octen-3-ol)

  Mrv1652305261923502D          

  9  8  0  0  0  0            999 V2000
    0.6336   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6349   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3480   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9204   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7770   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4914   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2059   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2059    0.5230    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  4  2  2  0  0  0  0
  5  3  1  0  0  0  0
  6  5  1  0  0  0  0
  7  6  1  0  0  0  0
  8  4  1  0  0  0  0
  8  7  1  0  0  0  0
  9  8  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0031299

> <DATABASE_NAME>
hmdb

> <SMILES>
CCCCCC(O)C=C

> <INCHI_IDENTIFIER>
InChI=1S/C8H16O/c1-3-5-6-7-8(9)4-2/h4,8-9H,2-3,5-7H2,1H3

> <INCHI_KEY>
VSMOENVRRABVKN-UHFFFAOYSA-N

> <FORMULA>
C8H16O

> <MOLECULAR_WEIGHT>
128.212

> <EXACT_MASS>
128.120115134

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
25

> <JCHEM_AVERAGE_POLARIZABILITY>
16.372748390837245

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
oct-1-en-3-ol

> <ALOGPS_LOGP>
2.43

> <JCHEM_LOGP>
2.4854761693333334

> <ALOGPS_LOGS>
-1.99

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
17.487640160517568

> <JCHEM_PKA_STRONGEST_BASIC>
-1.7107061937896155

> <JCHEM_POLAR_SURFACE_AREA>
20.23

> <JCHEM_REFRACTIVITY>
40.1698

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.31e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1-octen-3-ol

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0031299 ((R)-1-Octen-3-ol)

HMDB0031299
     RDKit          3D
(R)-1-Octen-3-ol
 25 24  0  0  0  0  0  0  0  0999 V2000
    2.9757   -1.6460   -0.5812 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4617   -0.6847   -1.3390 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8345    0.4781   -0.6485 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5579    0.7787    0.4907 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4179    0.0146   -0.2216 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2735    1.1434    0.4836 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6167    0.8954    1.0135 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7217    0.5057    0.1237 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5413   -0.8070   -0.5791 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4532   -2.5319   -1.0082 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9554   -1.6150    0.5054 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5146   -0.7765   -2.4023 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7585    1.3032   -1.3699 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4888    0.4240    0.3633 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1442   -0.2343   -1.1725 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4749   -0.9164    0.3577 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4455    1.4651    1.3092 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2253    2.0115   -0.2306 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5159    0.1082    1.8353 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9365    1.8479    1.5483 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6954    0.4380    0.7083 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9542    1.2701   -0.6631 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3579   -0.6577   -1.6671 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8007   -1.4729   -0.1249 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5551   -1.3417   -0.5580 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  2  3  1  0
  3  4  1  0
  3  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  1 10  1  0
  1 11  1  0
  2 12  1  0
  3 13  1  0
  4 14  1  0
  5 15  1  0
  5 16  1  0
  6 17  1  0
  6 18  1  0
  7 19  1  0
  7 20  1  0
  8 21  1  0
  8 22  1  0
  9 23  1  0
  9 24  1  0
  9 25  1  0
M  END
Download

PDB for HMDB0031299 ((R)-1-Octen-3-ol)

HEADER    PROTEIN                                 26-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   26-MAY-19         0                                  
HETATM    1  C   UNK     0       1.183  -1.334   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      10.518  -0.564   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.516  -0.564   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       9.185  -1.334   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.850  -1.334   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       5.184  -0.564   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       6.517  -1.334   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       7.851  -0.564   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       7.851   0.976   0.000  0.00  0.00           O+0
CONECT    1    3                                                            
CONECT    2    4                                                            
CONECT    3    1    5                                                       
CONECT    4    2    8                                                       
CONECT    5    3    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    4    7    9                                                  
CONECT    9    8                                                            
MASTER        0    0    0    0    0    0    0    0    9    0   16    0
END
Download

3D PDB for HMDB0031299 ((R)-1-Octen-3-ol)

COMPND    HMDB0031299
HETATM    1  C1  UNL     1       2.976  -1.646  -0.581  1.00  0.00           C  
HETATM    2  C2  UNL     1       2.462  -0.685  -1.339  1.00  0.00           C  
HETATM    3  C3  UNL     1       1.835   0.478  -0.649  1.00  0.00           C  
HETATM    4  O1  UNL     1       2.558   0.779   0.491  1.00  0.00           O  
HETATM    5  C4  UNL     1       0.418   0.015  -0.222  1.00  0.00           C  
HETATM    6  C5  UNL     1      -0.273   1.143   0.484  1.00  0.00           C  
HETATM    7  C6  UNL     1      -1.617   0.895   1.013  1.00  0.00           C  
HETATM    8  C7  UNL     1      -2.722   0.506   0.124  1.00  0.00           C  
HETATM    9  C8  UNL     1      -2.541  -0.807  -0.579  1.00  0.00           C  
HETATM   10  H1  UNL     1       3.453  -2.532  -1.008  1.00  0.00           H  
HETATM   11  H2  UNL     1       2.955  -1.615   0.505  1.00  0.00           H  
HETATM   12  H3  UNL     1       2.515  -0.776  -2.402  1.00  0.00           H  
HETATM   13  H4  UNL     1       1.758   1.303  -1.370  1.00  0.00           H  
HETATM   14  H5  UNL     1       3.489   0.424   0.363  1.00  0.00           H  
HETATM   15  H6  UNL     1      -0.144  -0.234  -1.172  1.00  0.00           H  
HETATM   16  H7  UNL     1       0.475  -0.916   0.358  1.00  0.00           H  
HETATM   17  H8  UNL     1       0.446   1.465   1.309  1.00  0.00           H  
HETATM   18  H9  UNL     1      -0.225   2.012  -0.231  1.00  0.00           H  
HETATM   19  H10 UNL     1      -1.516   0.108   1.835  1.00  0.00           H  
HETATM   20  H11 UNL     1      -1.937   1.848   1.548  1.00  0.00           H  
HETATM   21  H12 UNL     1      -3.695   0.438   0.708  1.00  0.00           H  
HETATM   22  H13 UNL     1      -2.954   1.270  -0.663  1.00  0.00           H  
HETATM   23  H14 UNL     1      -2.358  -0.658  -1.667  1.00  0.00           H  
HETATM   24  H15 UNL     1      -1.801  -1.473  -0.125  1.00  0.00           H  
HETATM   25  H16 UNL     1      -3.555  -1.342  -0.558  1.00  0.00           H  
CONECT    1    2    2   10   11
CONECT    2    3   12
CONECT    3    4    5   13
CONECT    4   14
CONECT    5    6   15   16
CONECT    6    7   17   18
CONECT    7    8   19   20
CONECT    8    9   21   22
CONECT    9   23   24   25
END
Download

SMILES for HMDB0031299 ((R)-1-Octen-3-ol)

CCCCCC(O)C=C
Download

INCHI for HMDB0031299 ((R)-1-Octen-3-ol)

InChI=1S/C8H16O/c1-3-5-6-7-8(9)4-2/h4,8-9H,2-3,5-7H2,1H3
Download
View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
1-Octen-3-olChEBI
1-VinylhexanolChEBI
3-Hydroxy-1-octeneChEBI
Mushroom alcoholChEBI
Octene-1-ol-3ChEBI
Vinyl amyl carbinolChEBI
Vinyl hexanolChEBI
1-Octen-3-ol, (+-)-isomerHMDB
1-Octen-3-ol, (R)-isomerHMDB
OctenolHMDB
Chemical FormulaC8H16O
Average Molecular Weight128.212
Monoisotopic Molecular Weight128.120115134
IUPAC Nameoct-1-en-3-ol
Traditional Name1-octen-3-ol
CAS Registry NumberNot Available
SMILES
CCCCCC(O)C=C
InChI Identifier
InChI=1S/C8H16O/c1-3-5-6-7-8(9)4-2/h4,8-9H,2-3,5-7H2,1H3
InChI KeyVSMOENVRRABVKN-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as fatty alcohols. These are aliphatic alcohols consisting of a chain of a least six carbon atoms.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassFatty Acyls
Sub ClassFatty alcohols
Direct ParentFatty alcohols
Alternative Parents
Substituents
  • Fatty alcohol
  • Secondary alcohol
  • Organic oxygen compound
  • Hydrocarbon derivative
  • Organooxygen compound
  • Alcohol
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationRoute of exposureSource
Process
Naturally occurring process
Role
Biological roleIndustrial application
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point175 °CNot Available
Boiling Point84.00 to 85.00 °C. @ 25.00 mm HgThe Good Scents Company Information System
Water Solubility1836 mg/L @ 25 °C (est)The Good Scents Company Information System
LogP2.519 (est)The Good Scents Company Information System
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
  • Membrane
Biospecimen Locations
  • Feces
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothNormal details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
FecesDetected but not QuantifiedNot QuantifiedNewborn (0-30 days old)Both
Normal		 details
FecesDetected and Quantified0-580340.894 nmol/g wet fecesChildren (1-13 years old)Not Specified
Normal		 details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothCrohn's disease details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothUlcerative colitis details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Campylobacter jejuni infection		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Clostridium difficile infection		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Ulcerative Colitis		 details
FecesDetected and Quantified0-443146.247 nmol/g wet fecesChildren (1-13 years old)Not Specified
Treated celiac disease		 details
Associated Disorders and Diseases
Disease References
Ulcerative colitis
  1. Garner CE, Smith S, de Lacy Costello B, White P, Spencer R, Probert CS, Ratcliffe NM: Volatile organic compounds from feces and their potential for diagnosis of gastrointestinal disease. FASEB J. 2007 Jun;21(8):1675-88. Epub 2007 Feb 21. [PubMed:17314143 ]
  2. Ahmed I, Greenwood R, Costello B, Ratcliffe N, Probert CS: Investigation of faecal volatile organic metabolites as novel diagnostic biomarkers in inflammatory bowel disease. Aliment Pharmacol Ther. 2016 Mar;43(5):596-611. doi: 10.1111/apt.13522. Epub 2016 Jan 25. [PubMed:26806034 ]
Celiac disease
  1. Di Cagno R, De Angelis M, De Pasquale I, Ndagijimana M, Vernocchi P, Ricciuti P, Gagliardi F, Laghi L, Crecchio C, Guerzoni ME, Gobbetti M, Francavilla R: Duodenal and faecal microbiota of celiac children: molecular, phenotype and metabolome characterization. BMC Microbiol. 2011 Oct 4;11:219. doi: 10.1186/1471-2180-11-219. [PubMed:21970810 ]
Crohn's disease
  1. Ahmed I, Greenwood R, Costello B, Ratcliffe N, Probert CS: Investigation of faecal volatile organic metabolites as novel diagnostic biomarkers in inflammatory bowel disease. Aliment Pharmacol Ther. 2016 Mar;43(5):596-611. doi: 10.1111/apt.13522. Epub 2016 Jan 25. [PubMed:26806034 ]
Associated OMIM IDs
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB003350
KNApSAcK IDC00029423
Chemspider ID17778
KEGG Compound IDC14272
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia Link1-Octen-3-ol
METLIN IDNot Available
PubChem Compound18827
PDB IDNot Available
ChEBI ID34118
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1024051
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Simons K, Toomre D: Lipid rafts and signal transduction. Nat Rev Mol Cell Biol. 2000 Oct;1(1):31-9. [PubMed:11413487 ]
  2. Watson AD: Thematic review series: systems biology approaches to metabolic and cardiovascular disorders. Lipidomics: a global approach to lipid analysis in biological systems. J Lipid Res. 2006 Oct;47(10):2101-11. Epub 2006 Aug 10. [PubMed:16902246 ]
  3. Sethi JK, Vidal-Puig AJ: Thematic review series: adipocyte biology. Adipose tissue function and plasticity orchestrate nutritional adaptation. J Lipid Res. 2007 Jun;48(6):1253-62. Epub 2007 Mar 20. [PubMed:17374880 ]
  4. Lingwood D, Simons K: Lipid rafts as a membrane-organizing principle. Science. 2010 Jan 1;327(5961):46-50. doi: 10.1126/science.1174621. [PubMed:20044567 ]
  5. (). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .
  6. Gunstone, Frank D., John L. Harwood, and Albert J. Dijkstra (2007). The lipid handbook with CD-ROM. CRC Press.