Hmdb loader

Showing metabocard for cis-Ocimene (HMDB0030088)

Jump To Section:
IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesXML
Show more...Show more...Show more...Show more...
Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2012-09-11 17:34:41 UTC
Update Date2022-03-07 02:52:25 UTC
HMDB IDHMDB0030088
Secondary Accession Numbers
  • HMDB30088
Metabolite Identification
Common Namecis-Ocimene
Descriptioncis-Ocimene is found in allspice. Ocimene refers to several isomeric hydrocarbons. The ocimenes are monoterpenes found within a variety of plants and fruits. alpha-Ocimene and the two beta-ocimenes differ in the position of the isolated double bond: it is terminal in the alpha isomer. alpha-Ocimene is 3,7-dimethyl-1,3,7-octatriene. beta-Ocimene is 3,7-dimethyl-1,3,6-octatriene. beta-Ocimene exists in two stereoisomeric forms, cis and trans, with respect to the central double bond. The ocimenes are often found naturally as mixtures of the various forms. The mixture (as well as the pure compounds) is an oil with a pleasant odor. It is used in perfumery. (Wikipedia
Structure
Data?1563861935
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0030088 (cis-Ocimene)

  Mrv1652303202019002D          

 10  9  0  0  0  0            999 V2000
    1.3753   -3.8166    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0898   -3.4041    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8043   -3.8166    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0898   -2.5791    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3753   -4.6416    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0898   -5.0541    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0898   -5.8791    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8043   -6.2916    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3753   -6.2916    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8043   -4.6416    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  1  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  7  9  1  0  0  0  0
  3 10  2  0  0  0  0
M  END
Download

3D MOL for HMDB0030088 (cis-Ocimene)

HMDB0030088
     RDKit          3D
cis-Ocimene
 26 25  0  0  0  0  0  0  0  0999 V2000
   -3.9431   -0.0112    0.7961 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6341   -0.2174    0.5792 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0061    0.1107   -0.6703 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8180    0.7141   -1.8078 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7340   -0.0691   -0.9387 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1869   -0.6490    0.0693 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2571    0.3432    0.3928 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5272    0.0354    0.1769 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5849    1.0606    0.5146 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9496   -1.2707   -0.3809 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4193   -0.2564    1.7337 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5092    0.4194   -0.0247 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0885   -0.6365    1.3893 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3038    0.5547   -2.7766 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7582    0.0957   -1.8886 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0174    1.7585   -1.5665 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3312    0.2145   -1.9357 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7129   -1.5414   -0.4144 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2854   -1.0444    0.9539 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9599    1.2942    0.7982 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3557    1.5396    1.4899 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5783    1.7753   -0.3328 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5801    0.5878    0.5414 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0541   -1.3094   -0.4201 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5554   -2.1056    0.2532 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5461   -1.3924   -1.4065 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  3  5  2  0
  5  6  1  0
  6  7  1  0
  7  8  2  3
  8  9  1  0
  8 10  1  0
  1 11  1  0
  1 12  1  0
  2 13  1  0
  4 14  1  0
  4 15  1  0
  4 16  1  0
  5 17  1  0
  6 18  1  0
  6 19  1  0
  7 20  1  0
  9 21  1  0
  9 22  1  0
  9 23  1  0
 10 24  1  0
 10 25  1  0
 10 26  1  0
M  END
Download

3D SDF for HMDB0030088 (cis-Ocimene)

  Mrv1652303202019002D          

 10  9  0  0  0  0            999 V2000
    1.3753   -3.8166    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0898   -3.4041    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8043   -3.8166    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0898   -2.5791    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3753   -4.6416    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0898   -5.0541    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0898   -5.8791    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8043   -6.2916    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3753   -6.2916    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8043   -4.6416    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  1  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  7  9  1  0  0  0  0
  3 10  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0030088

> <DATABASE_NAME>
hmdb

> <SMILES>
CC(C)=CC\C=C(\C)C=C

> <INCHI_IDENTIFIER>
InChI=1S/C10H16/c1-5-10(4)8-6-7-9(2)3/h5,7-8H,1,6H2,2-4H3/b10-8-

> <INCHI_KEY>
IHPKGUQCSIINRJ-NTMALXAHSA-N

> <FORMULA>
C10H16

> <MOLECULAR_WEIGHT>
136.234

> <EXACT_MASS>
136.125200512

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_ATOM_COUNT>
26

> <JCHEM_AVERAGE_POLARIZABILITY>
17.18387789242175

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3Z)-3,7-dimethylocta-1,3,6-triene

> <ALOGPS_LOGP>
4.30

> <JCHEM_LOGP>
3.479166466333333

> <ALOGPS_LOGS>
-2.91

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_POLAR_SURFACE_AREA>
0.0

> <JCHEM_REFRACTIVITY>
49.451499999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.67e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(Z)-β-ocimene

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0030088 (cis-Ocimene)

HMDB0030088
     RDKit          3D
cis-Ocimene
 26 25  0  0  0  0  0  0  0  0999 V2000
   -3.9431   -0.0112    0.7961 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6341   -0.2174    0.5792 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0061    0.1107   -0.6703 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8180    0.7141   -1.8078 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7340   -0.0691   -0.9387 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1869   -0.6490    0.0693 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2571    0.3432    0.3928 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5272    0.0354    0.1769 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5849    1.0606    0.5146 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9496   -1.2707   -0.3809 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4193   -0.2564    1.7337 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5092    0.4194   -0.0247 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0885   -0.6365    1.3893 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3038    0.5547   -2.7766 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7582    0.0957   -1.8886 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0174    1.7585   -1.5665 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3312    0.2145   -1.9357 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7129   -1.5414   -0.4144 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2854   -1.0444    0.9539 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9599    1.2942    0.7982 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3557    1.5396    1.4899 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5783    1.7753   -0.3328 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5801    0.5878    0.5414 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0541   -1.3094   -0.4201 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5554   -2.1056    0.2532 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5461   -1.3924   -1.4065 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  3  5  2  0
  5  6  1  0
  6  7  1  0
  7  8  2  3
  8  9  1  0
  8 10  1  0
  1 11  1  0
  1 12  1  0
  2 13  1  0
  4 14  1  0
  4 15  1  0
  4 16  1  0
  5 17  1  0
  6 18  1  0
  6 19  1  0
  7 20  1  0
  9 21  1  0
  9 22  1  0
  9 23  1  0
 10 24  1  0
 10 25  1  0
 10 26  1  0
M  END
Download

PDB for HMDB0030088 (cis-Ocimene)

HEADER    PROTEIN                                 20-MAR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   20-MAR-20         0                                  
HETATM    1  C   UNK     0       2.567  -7.124   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       3.901  -6.354   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.235  -7.124   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.901  -4.814   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.567  -8.664   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       3.901  -9.434   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.901 -10.974   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       5.235 -11.744   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.567 -11.744   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       5.235  -8.664   0.000  0.00  0.00           C+0
CONECT    1    2    5                                                       
CONECT    2    1    3    4                                                  
CONECT    3    2   10                                                       
CONECT    4    2                                                            
CONECT    5    1    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7                                                            
CONECT   10    3                                                            
MASTER        0    0    0    0    0    0    0    0   10    0   18    0
END
Download

3D PDB for HMDB0030088 (cis-Ocimene)

COMPND    HMDB0030088
HETATM    1  C1  UNL     1      -3.943  -0.011   0.796  1.00  0.00           C  
HETATM    2  C2  UNL     1      -2.634  -0.217   0.579  1.00  0.00           C  
HETATM    3  C3  UNL     1      -2.006   0.111  -0.670  1.00  0.00           C  
HETATM    4  C4  UNL     1      -2.818   0.714  -1.808  1.00  0.00           C  
HETATM    5  C5  UNL     1      -0.734  -0.069  -0.939  1.00  0.00           C  
HETATM    6  C6  UNL     1       0.187  -0.649   0.069  1.00  0.00           C  
HETATM    7  C7  UNL     1       1.257   0.343   0.393  1.00  0.00           C  
HETATM    8  C8  UNL     1       2.527   0.035   0.177  1.00  0.00           C  
HETATM    9  C9  UNL     1       3.585   1.061   0.515  1.00  0.00           C  
HETATM   10  C10 UNL     1       2.950  -1.271  -0.381  1.00  0.00           C  
HETATM   11  H1  UNL     1      -4.419  -0.256   1.734  1.00  0.00           H  
HETATM   12  H2  UNL     1      -4.509   0.419  -0.025  1.00  0.00           H  
HETATM   13  H3  UNL     1      -2.089  -0.637   1.389  1.00  0.00           H  
HETATM   14  H4  UNL     1      -2.304   0.555  -2.777  1.00  0.00           H  
HETATM   15  H5  UNL     1      -3.758   0.096  -1.889  1.00  0.00           H  
HETATM   16  H6  UNL     1      -3.017   1.758  -1.566  1.00  0.00           H  
HETATM   17  H7  UNL     1      -0.331   0.215  -1.936  1.00  0.00           H  
HETATM   18  H8  UNL     1       0.713  -1.541  -0.414  1.00  0.00           H  
HETATM   19  H9  UNL     1      -0.285  -1.044   0.954  1.00  0.00           H  
HETATM   20  H10 UNL     1       0.960   1.294   0.798  1.00  0.00           H  
HETATM   21  H11 UNL     1       3.356   1.540   1.490  1.00  0.00           H  
HETATM   22  H12 UNL     1       3.578   1.775  -0.333  1.00  0.00           H  
HETATM   23  H13 UNL     1       4.580   0.588   0.541  1.00  0.00           H  
HETATM   24  H14 UNL     1       4.054  -1.309  -0.420  1.00  0.00           H  
HETATM   25  H15 UNL     1       2.555  -2.106   0.253  1.00  0.00           H  
HETATM   26  H16 UNL     1       2.546  -1.392  -1.406  1.00  0.00           H  
CONECT    1    2    2   11   12
CONECT    2    3   13
CONECT    3    4    5    5
CONECT    4   14   15   16
CONECT    5    6   17
CONECT    6    7   18   19
CONECT    7    8    8   20
CONECT    8    9   10
CONECT    9   21   22   23
CONECT   10   24   25   26
END
Download

SMILES for HMDB0030088 (cis-Ocimene)

CC(C)=CC\C=C(\C)C=C
Download

INCHI for HMDB0030088 (cis-Ocimene)

InChI=1S/C10H16/c1-5-10(4)8-6-7-9(2)3/h5,7-8H,1,6H2,2-4H3/b10-8-
Download
View in JSmolView Stereo Labels
Synonyms
Chemical FormulaC10H16
Average Molecular Weight136.234
Monoisotopic Molecular Weight136.125200512
IUPAC Name(3Z)-3,7-dimethylocta-1,3,6-triene
Traditional Name(Z)-β-ocimene
CAS Registry Number3338-55-4
SMILES
CC(C)=CC\C=C(\C)C=C
InChI Identifier
InChI=1S/C10H16/c1-5-10(4)8-6-7-9(2)3/h5,7-8H,1,6H2,2-4H3/b10-8-
InChI KeyIHPKGUQCSIINRJ-NTMALXAHSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as acyclic monoterpenoids. These are monoterpenes that do not contain a cycle.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassPrenol lipids
Sub ClassMonoterpenoids
Direct ParentAcyclic monoterpenoids
Alternative Parents
Substituents
  • Acyclic monoterpenoid
  • Branched unsaturated hydrocarbon
  • Alkatriene
  • Unsaturated aliphatic hydrocarbon
  • Unsaturated hydrocarbon
  • Olefin
  • Acyclic olefin
  • Hydrocarbon
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effect
Organoleptic effect
Disposition
Biological locationRoute of exposureSource
Process
Naturally occurring process
Role
Industrial applicationBiological role
Physical Properties
StateLiquid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling Point177.00 °C. @ 760.00 mm HgThe Good Scents Company Information System
Water Solubility2.01 mg/L @ 25 °C (est)The Good Scents Company Information System
LogP4.700 (est)The Good Scents Company Information System
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Extracellular
  • Membrane
Biospecimen Locations
  • Saliva
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Not SpecifiedNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB001462
KNApSAcK IDC00000843
Chemspider ID4478390
KEGG Compound IDNot Available
BioCyc IDCPD-4903
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound5320250
PDB IDNot Available
ChEBI ID87574
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1010541
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. (). Afendi FM, Okada T, Yamazaki M, Hirai-Morita A, Nakamura Y, Nakamura K, Ikeda S, Takahashi H, Altaf-Ul-Amin M, Darusman LK, Saito K, Kanaya S. (2012) KNApSAcK family databases: integrated metabolite-plant species databases for multifaceted plant research. Plant Cell Physiol. 2012 Feb;53(2):e1.. .
  6. Gunstone, Frank D., John L. Harwood, and Albert J. Dijkstra (2007). The lipid handbook with CD-ROM. CRC Press.