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Showing metabocard for 3-Hexen-1-ol (HMDB0030003)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-11 17:34:06 UTC
Update Date2023-02-21 17:19:24 UTC
HMDB IDHMDB0030003
Secondary Accession Numbers
  • HMDB30003
Metabolite Identification
Common Name3-Hexen-1-ol
Description3-Hexen-1-ol, also known as 1-hydroxy-3-hexene, is a colourless oily liquid with an intense grassy-green odour of freshly cut green grass and leaves. It is produced in small amounts by most plants and it acts as an attractant to many predatory insects. 3-Hexen-1-ol is a very important aroma compound that is used in fruit and vegetable flavours and in perfumes. The yearly production is about 30 tonnes. 3-Hexen-1-ol is found in black elderberry.
Structure
Data?1676999964
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0030003 (3-Hexen-1-ol)

  Mrv1652309272007332D          

  7  6  0  0  0  0            999 V2000
10009.486110007.7791    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10010.200610007.3668    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10011.025610007.3668    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10011.740410007.7791    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10012.454810007.3668    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10013.169410007.7791    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10008.771110007.3661    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  1  7  1  0  0  0  0
M  END
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3D MOL for HMDB0030003 (3-Hexen-1-ol)

HMDB0030003
     RDKit          3D
3-Hexen-1-ol
 19 18  0  0  0  0  0  0  0  0999 V2000
   -2.8620    0.4957    0.1468 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5575    0.1877   -0.6019 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9003   -1.0059   -0.1056 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2937   -1.0398    0.4037 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1397    0.1492    0.5424 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4206   -0.0630   -0.2574 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2105    1.0912   -0.1059 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6618    0.9682    1.1204 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3912    1.2539   -0.4826 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4642   -0.4201    0.2319 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9349   -0.0000   -1.6615 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9830    1.1113   -0.6606 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4402   -1.9688   -0.1565 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7435   -1.9831    0.7662 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4497    0.1871    1.6299 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7254    1.1058    0.2697 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1926   -0.1429   -1.3371 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0026   -0.9237    0.1037 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0166    0.9972   -0.6598 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  1  8  1  0
  1  9  1  0
  1 10  1  0
  2 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
M  END
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3D SDF for HMDB0030003 (3-Hexen-1-ol)

  Mrv1652309272007332D          

  7  6  0  0  0  0            999 V2000
10009.486110007.7791    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10010.200610007.3668    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10011.025610007.3668    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10011.740410007.7791    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10012.454810007.3668    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10013.169410007.7791    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10008.771110007.3661    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  1  7  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0030003

> <DATABASE_NAME>
hmdb

> <SMILES>
CC\C=C/CCO

> <INCHI_IDENTIFIER>
InChI=1S/C6H12O/c1-2-3-4-5-6-7/h3-4,7H,2,5-6H2,1H3/b4-3-

> <INCHI_KEY>
UFLHIIWVXFIJGU-ARJAWSKDSA-N

> <FORMULA>
C6H12O

> <MOLECULAR_WEIGHT>
100.1589

> <EXACT_MASS>
100.088815006

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
19

> <JCHEM_AVERAGE_POLARIZABILITY>
12.279776103805364

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3Z)-hex-3-en-1-ol

> <ALOGPS_LOGP>
1.69

> <JCHEM_LOGP>
1.3325376193333331

> <ALOGPS_LOGS>
-0.79

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
16.791790810402865

> <JCHEM_PKA_STRONGEST_BASIC>
-2.015070699529785

> <JCHEM_POLAR_SURFACE_AREA>
20.23

> <JCHEM_REFRACTIVITY>
32.4535

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.62e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
cis-3-hexenol

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0030003 (3-Hexen-1-ol)

HMDB0030003
     RDKit          3D
3-Hexen-1-ol
 19 18  0  0  0  0  0  0  0  0999 V2000
   -2.8620    0.4957    0.1468 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5575    0.1877   -0.6019 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9003   -1.0059   -0.1056 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2937   -1.0398    0.4037 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1397    0.1492    0.5424 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4206   -0.0630   -0.2574 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2105    1.0912   -0.1059 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6618    0.9682    1.1204 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3912    1.2539   -0.4826 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4642   -0.4201    0.2319 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9349   -0.0000   -1.6615 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9830    1.1113   -0.6606 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4402   -1.9688   -0.1565 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7435   -1.9831    0.7662 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4497    0.1871    1.6299 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7254    1.1058    0.2697 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1926   -0.1429   -1.3371 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0026   -0.9237    0.1037 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0166    0.9972   -0.6598 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  1  8  1  0
  1  9  1  0
  1 10  1  0
  2 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
M  END
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PDB for HMDB0030003 (3-Hexen-1-ol)

HEADER    PROTEIN                                 27-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-SEP-20         0                                  
HETATM    1  C   UNK     0    8684.3748681.188   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0    8685.7088680.418   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0    8687.2488680.418   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0    8688.5828681.188   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0    8689.9168680.418   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0    8691.2508681.188   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0    8683.0398680.417   0.000  0.00  0.00           C+0
CONECT    1    2    7                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5                                                            
CONECT    7    1                                                            
MASTER        0    0    0    0    0    0    0    0    7    0   12    0
END
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3D PDB for HMDB0030003 (3-Hexen-1-ol)

COMPND    HMDB0030003
HETATM    1  C1  UNL     1      -2.862   0.496   0.147  1.00  0.00           C  
HETATM    2  C2  UNL     1      -1.558   0.188  -0.602  1.00  0.00           C  
HETATM    3  C3  UNL     1      -0.900  -1.006  -0.106  1.00  0.00           C  
HETATM    4  C4  UNL     1       0.294  -1.040   0.404  1.00  0.00           C  
HETATM    5  C5  UNL     1       1.140   0.149   0.542  1.00  0.00           C  
HETATM    6  C6  UNL     1       2.421  -0.063  -0.257  1.00  0.00           C  
HETATM    7  O1  UNL     1       3.211   1.091  -0.106  1.00  0.00           O  
HETATM    8  H1  UNL     1      -2.662   0.968   1.120  1.00  0.00           H  
HETATM    9  H2  UNL     1      -3.391   1.254  -0.483  1.00  0.00           H  
HETATM   10  H3  UNL     1      -3.464  -0.420   0.232  1.00  0.00           H  
HETATM   11  H4  UNL     1      -1.935  -0.000  -1.662  1.00  0.00           H  
HETATM   12  H5  UNL     1      -0.983   1.111  -0.661  1.00  0.00           H  
HETATM   13  H6  UNL     1      -1.440  -1.969  -0.157  1.00  0.00           H  
HETATM   14  H7  UNL     1       0.743  -1.983   0.766  1.00  0.00           H  
HETATM   15  H8  UNL     1       1.450   0.187   1.630  1.00  0.00           H  
HETATM   16  H9  UNL     1       0.725   1.106   0.270  1.00  0.00           H  
HETATM   17  H10 UNL     1       2.193  -0.143  -1.337  1.00  0.00           H  
HETATM   18  H11 UNL     1       3.003  -0.924   0.104  1.00  0.00           H  
HETATM   19  H12 UNL     1       4.017   0.997  -0.660  1.00  0.00           H  
CONECT    1    2    8    9   10
CONECT    2    3   11   12
CONECT    3    4    4   13
CONECT    4    5   14
CONECT    5    6   15   16
CONECT    6    7   17   18
CONECT    7   19
END
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SMILES for HMDB0030003 (3-Hexen-1-ol)

CC\C=C/CCO
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INCHI for HMDB0030003 (3-Hexen-1-ol)

InChI=1S/C6H12O/c1-2-3-4-5-6-7/h3-4,7H,2,5-6H2,1H3/b4-3-
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
Chemical FormulaC6H12O
Average Molecular Weight100.1589
Monoisotopic Molecular Weight100.088815006
IUPAC Name(3Z)-hex-3-en-1-ol
Traditional Namecis-3-hexenol
CAS Registry Number928-96-1
SMILES
CC\C=C/CCO
InChI Identifier
InChI=1S/C6H12O/c1-2-3-4-5-6-7/h3-4,7H,2,5-6H2,1H3/b4-3-
InChI KeyUFLHIIWVXFIJGU-ARJAWSKDSA-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
  • Organic oxygen compound
  • Hydrocarbon derivative
  • Primary alcohol
  • Organooxygen compound
  • Alcohol
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effect
Organoleptic effect
Disposition
Biological locationRoute of exposureSource
Process
Naturally occurring process
Role
Biological roleIndustrial application
Physical Properties
StateLiquid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling Point156.50 °C. @ 760.00 mm HgThe Good Scents Company Information System
Water Solubility16000 mg/L @ 25 °C (est)The Good Scents Company Information System
LogP1.697 (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 LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB008091
KNApSAcK IDC00000356
Chemspider ID21105914
KEGG Compound IDC08492
BioCyc IDCIS-3-HEXENOL
BiGG IDNot Available
Wikipedia LinkCis-3-Hexen-1-ol
METLIN IDNot Available
PubChem Compound5281167
PDB IDNot Available
ChEBI ID28857
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1005931
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.