Showing metabocard for (z)-Ocimene (MMDBc0047628)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2021-11-19 15:34:53 UTC
Update Date2024-04-30 20:28:19 UTC
Metabolite IDMMDBc0047628
Metabolite Identification
Common Name(z)-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
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007fed15351ec0>


  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 #<Metabolite:0x00007fed15351ec0>

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 #<Metabolite:0x00007fed15351ec0>


  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>
MMDBc0047628

> <DATABASE_NAME>
MIME

> <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

$$$$
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3D-SDF for #<Metabolite:0x00007fed15351ec0>

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
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PDB for #<Metabolite:0x00007fed15351ec0>

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
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3D PDB for #<Metabolite:0x00007fed15351ec0>

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
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SMILES for #<Metabolite:0x00007fed15351ec0>

CC(C)=CC\C=C(\C)C=C
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INCHI for #<Metabolite:0x00007fed15351ec0>

InChI=1S/C10H16/c1-5-10(4)8-6-7-9(2)3/h5,7-8H,1,6H2,2-4H3/b10-8-
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Synonyms
ValueSource
beta-cis-OcimeneChEBI
cis-3,7-Dimethyl-1,3,6-octatrieneChEBI
b-cis-OcimeneGenerator
Β-cis-ocimeneGenerator
cis-&beta;-ocimeneMetaCyc, HMDB
(3Z)-3,7-Dimethyl-1,3,6-octatrieneHMDB
(Z)-3,7-Dimethyl-1,3,6-octatrieneHMDB
(Z)-3,7-Dimethylocta-1,3,6,-trieneHMDB
(Z)-beta-OcimeneHMDB
3,7-Dimethyl-(3Z)-1,3,6-octatrieneHMDB
3,7-Dimethyl-(Z)-1,3,6-octatrieneHMDB
beta -(Z)-OcimeneHMDB
beta -cis-OcimeneHMDB
cis-beta -OcimeneHMDB
cis-beta-OcimeneHMDB
Z-beta -OcimeneHMDB
Z-OcimeneHMDB
(Z)-b-OcimeneGenerator
(Z)-Β-ocimeneGenerator
cis-b-OcimeneGenerator
cis-Β-ocimeneGenerator
Molecular FormulaC10H16
Average Mass136.234
Monoisotopic Mass136.125200512
IUPAC Name(3Z)-3,7-dimethylocta-1,3,6-triene
Traditional Name(Z)-β-ocimene
CAS Registry NumberNot Available
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