Hmdb loader

Showing metabocard for D-Citronellol (HMDB0035093)

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IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesXML
Record Information
Version5.0
StatusDetected and Quantified
Creation Date2012-09-11 20:02:11 UTC
Update Date2023-02-21 17:24:36 UTC
HMDB IDHMDB0035093
Secondary Accession Numbers
  • HMDB35093
Metabolite Identification
Common NameD-Citronellol
DescriptionCitronellol is formally classified as alkylalcohol although it is biochemically a monoterpenoid as it is synthesized from isoprene units. Citronellol is a neutral compound. It is a naturally occurring organic compound found in cannabis plants (PMID:6991645 ). Citronellol occurs in many essential oils as either - or + enantiomers. -Citronellol is found in the oils of rose (18-55%) and Pelargonium geraniums while + citronellol is found in citronella oils extracted from the leaves and stems of Cymbopogon nardus or citronella grass. Citronellol has a citrus, floral, and geranium taste with a floral leathery waxy rose citrus odor ( Ref:DOI). It is used in perfumery to add scents to soaps and incense. It is an insect repellent that repels mosquitos at short distances (PMID:2862274 ). Citronellol is found in highest concentrations in gingers, sweet basils, and winter savories and in lower concentrations in highbush blueberries, bilberries, and cardamoms. Citronellol has also been detected in blackcurrants, fennels, evergreen blackberries, herbs and spices, and nutmegs making citronellol a potential biomarker for the consumption of these foods. Citronellol has promising pharmacological activities (PMID:30453001 ) against human lung cancer (PMID:31280209 ), against induced rat breast cancer (PMID:31313341 ), has antifungal activity against Candida species (PMID:32150884 ) and has anti-hypertensive properties (PMID:26872991 ).
Structure
Data?1677000276
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0035093 (D-Citronellol)


  Mrv1652305271900072D          

 11 10  0  0  0  0            999 V2000
10001.371210000.4542    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
10000.656010000.0428    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.940610000.4542    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.226310000.0428    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.511710000.4542    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9997.797410000.0428    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.511710001.2792    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10002.086410000.0428    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10002.799510000.4542    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10003.514710000.0428    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10001.371210001.2792    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  8  1  0  0  0  0
  1 11  1  1  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  5  7  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
M  END
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3D MOL for HMDB0035093 (D-Citronellol)

HMDB0035093
     RDKit          3D
D-Citronellol
 31 30  0  0  0  0  0  0  0  0999 V2000
    3.9907    1.1869    0.7742 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9354    0.3788    0.1050 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2580   -0.2048   -1.2375 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7680    0.1898    0.6779 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6828   -0.6054    0.0566 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5775    0.2288   -0.1638 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5895   -0.7019   -0.7972 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.8578   -1.8365    0.1095 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7697    0.0330   -1.3082 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5552    0.8066   -0.3200 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8086    1.7939    0.3139 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1093    2.1864    0.3309 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7906    1.2605    1.8751 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9524    0.6307    0.6584 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2046   -1.3183   -1.1102 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2862    0.0206   -1.5432 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5563    0.1514   -1.9927 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5702    0.6271    1.6492 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0540   -1.0154   -0.9065 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4005   -1.4492    0.6924 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9704    0.4738    0.8599 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3819    1.1305   -0.7527 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0607   -1.1230   -1.7052 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7146   -1.4923    1.1722 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8441   -2.3174   -0.0003 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1002   -2.6353   -0.0343 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4680   -0.6102   -1.8824 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3870    0.7733   -2.0729 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3479    1.3656   -0.9019 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1268    0.1883    0.4005 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9991    1.8838    1.2640 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  2  3
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
 10 11  1  0
  1 12  1  0
  1 13  1  0
  1 14  1  0
  3 15  1  0
  3 16  1  0
  3 17  1  0
  4 18  1  0
  5 19  1  0
  5 20  1  0
  6 21  1  0
  6 22  1  0
  7 23  1  6
  8 24  1  0
  8 25  1  0
  8 26  1  0
  9 27  1  0
  9 28  1  0
 10 29  1  0
 10 30  1  0
 11 31  1  0
M  END
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3D SDF for HMDB0035093 (D-Citronellol)


  Mrv1652305271900072D          

 11 10  0  0  0  0            999 V2000
10001.371210000.4542    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
10000.656010000.0428    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.940610000.4542    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.226310000.0428    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.511710000.4542    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9997.797410000.0428    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.511710001.2792    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10002.086410000.0428    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10002.799510000.4542    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10003.514710000.0428    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10001.371210001.2792    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  8  1  0  0  0  0
  1 11  1  1  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  5  7  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0035093

> <DATABASE_NAME>
hmdb

> <SMILES>
C[C@@H](CCO)CCC=C(C)C

> <INCHI_IDENTIFIER>
InChI=1S/C10H20O/c1-9(2)5-4-6-10(3)7-8-11/h5,10-11H,4,6-8H2,1-3H3/t10-/m1/s1

> <INCHI_KEY>
QMVPMAAFGQKVCJ-SNVBAGLBSA-N

> <FORMULA>
C10H20O

> <MOLECULAR_WEIGHT>
156.2652

> <EXACT_MASS>
156.151415262

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
31

> <JCHEM_AVERAGE_POLARIZABILITY>
20.076468200897626

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3R)-3,7-dimethyloct-6-en-1-ol

> <ALOGPS_LOGP>
3.48

> <JCHEM_LOGP>
2.752055317333333

> <ALOGPS_LOGS>
-2.27

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
17.10979181623922

> <JCHEM_PKA_STRONGEST_BASIC>
-1.8759770595769654

> <JCHEM_POLAR_SURFACE_AREA>
20.23

> <JCHEM_REFRACTIVITY>
50.48609999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.46e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
β-citronellol

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0035093 (D-Citronellol)

HMDB0035093
     RDKit          3D
D-Citronellol
 31 30  0  0  0  0  0  0  0  0999 V2000
    3.9907    1.1869    0.7742 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9354    0.3788    0.1050 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2580   -0.2048   -1.2375 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7680    0.1898    0.6779 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6828   -0.6054    0.0566 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5775    0.2288   -0.1638 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5895   -0.7019   -0.7972 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.8578   -1.8365    0.1095 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7697    0.0330   -1.3082 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5552    0.8066   -0.3200 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8086    1.7939    0.3139 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1093    2.1864    0.3309 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7906    1.2605    1.8751 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9524    0.6307    0.6584 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2046   -1.3183   -1.1102 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2862    0.0206   -1.5432 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5563    0.1514   -1.9927 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5702    0.6271    1.6492 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0540   -1.0154   -0.9065 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4005   -1.4492    0.6924 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9704    0.4738    0.8599 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3819    1.1305   -0.7527 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0607   -1.1230   -1.7052 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7146   -1.4923    1.1722 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8441   -2.3174   -0.0003 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1002   -2.6353   -0.0343 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4680   -0.6102   -1.8824 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3870    0.7733   -2.0729 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3479    1.3656   -0.9019 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1268    0.1883    0.4005 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9991    1.8838    1.2640 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  2  3
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
 10 11  1  0
  1 12  1  0
  1 13  1  0
  1 14  1  0
  3 15  1  0
  3 16  1  0
  3 17  1  0
  4 18  1  0
  5 19  1  0
  5 20  1  0
  6 21  1  0
  6 22  1  0
  7 23  1  6
  8 24  1  0
  8 25  1  0
  8 26  1  0
  9 27  1  0
  9 28  1  0
 10 29  1  0
 10 30  1  0
 11 31  1  0
M  END
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PDB for HMDB0035093 (D-Citronellol)

HEADER    PROTEIN                                 27-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-MAY-19         0                                  
HETATM    1  C   UNK     0    8669.2268667.515   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0    8667.8918666.747   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0    8666.5568667.515   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0    8665.2228666.747   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0    8663.8898667.515   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0    8662.5558666.747   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0    8663.8898669.055   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0    8670.5618666.747   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0    8671.8928667.515   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0    8673.2278666.747   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0    8669.2268669.055   0.000  0.00  0.00           C+0
CONECT    1    2    8   11                                                  
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5                                                            
CONECT    8    1    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9                                                            
CONECT   11    1                                                            
MASTER        0    0    0    0    0    0    0    0   11    0   20    0
END
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3D PDB for HMDB0035093 (D-Citronellol)

COMPND    HMDB0035093
HETATM    1  C1  UNL     1       3.991   1.187   0.774  1.00  0.00           C  
HETATM    2  C2  UNL     1       2.935   0.379   0.105  1.00  0.00           C  
HETATM    3  C3  UNL     1       3.258  -0.205  -1.237  1.00  0.00           C  
HETATM    4  C4  UNL     1       1.768   0.190   0.678  1.00  0.00           C  
HETATM    5  C5  UNL     1       0.683  -0.605   0.057  1.00  0.00           C  
HETATM    6  C6  UNL     1      -0.578   0.229  -0.164  1.00  0.00           C  
HETATM    7  C7  UNL     1      -1.589  -0.702  -0.797  1.00  0.00           C  
HETATM    8  C8  UNL     1      -1.858  -1.837   0.109  1.00  0.00           C  
HETATM    9  C9  UNL     1      -2.770   0.033  -1.308  1.00  0.00           C  
HETATM   10  C10 UNL     1      -3.555   0.807  -0.320  1.00  0.00           C  
HETATM   11  O1  UNL     1      -2.809   1.794   0.314  1.00  0.00           O  
HETATM   12  H1  UNL     1       4.109   2.186   0.331  1.00  0.00           H  
HETATM   13  H2  UNL     1       3.791   1.261   1.875  1.00  0.00           H  
HETATM   14  H3  UNL     1       4.952   0.631   0.658  1.00  0.00           H  
HETATM   15  H4  UNL     1       3.205  -1.318  -1.110  1.00  0.00           H  
HETATM   16  H5  UNL     1       4.286   0.021  -1.543  1.00  0.00           H  
HETATM   17  H6  UNL     1       2.556   0.151  -1.993  1.00  0.00           H  
HETATM   18  H7  UNL     1       1.570   0.627   1.649  1.00  0.00           H  
HETATM   19  H8  UNL     1       1.054  -1.015  -0.907  1.00  0.00           H  
HETATM   20  H9  UNL     1       0.401  -1.449   0.692  1.00  0.00           H  
HETATM   21  H10 UNL     1      -0.970   0.474   0.860  1.00  0.00           H  
HETATM   22  H11 UNL     1      -0.382   1.131  -0.753  1.00  0.00           H  
HETATM   23  H12 UNL     1      -1.061  -1.123  -1.705  1.00  0.00           H  
HETATM   24  H13 UNL     1      -1.715  -1.492   1.172  1.00  0.00           H  
HETATM   25  H14 UNL     1      -2.844  -2.317  -0.000  1.00  0.00           H  
HETATM   26  H15 UNL     1      -1.100  -2.635  -0.034  1.00  0.00           H  
HETATM   27  H16 UNL     1      -3.468  -0.610  -1.882  1.00  0.00           H  
HETATM   28  H17 UNL     1      -2.387   0.773  -2.073  1.00  0.00           H  
HETATM   29  H18 UNL     1      -4.348   1.366  -0.902  1.00  0.00           H  
HETATM   30  H19 UNL     1      -4.127   0.188   0.400  1.00  0.00           H  
HETATM   31  H20 UNL     1      -2.999   1.884   1.264  1.00  0.00           H  
CONECT    1    2   12   13   14
CONECT    2    3    4    4
CONECT    3   15   16   17
CONECT    4    5   18
CONECT    5    6   19   20
CONECT    6    7   21   22
CONECT    7    8    9   23
CONECT    8   24   25   26
CONECT    9   10   27   28
CONECT   10   11   29   30
CONECT   11   31
END
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SMILES for HMDB0035093 (D-Citronellol)

C[C@@H](CCO)CCC=C(C)C
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INCHI for HMDB0035093 (D-Citronellol)

InChI=1S/C10H20O/c1-9(2)5-4-6-10(3)7-8-11/h5,10-11H,4,6-8H2,1-3H3/t10-/m1/s1
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Synonyms
ValueSource
(R)-(+)-CitronellolKegg
(+)-beta-CitronellolHMDB
(+)-R-CitronellolHMDB
(3R)-3,7-Dimethyloct-6-en-1-olHMDB
(R)-(+)-beta -CitronellolHMDB
(R)-(+)-beta-CitronellolHMDB
(R)-3,7-Dimethyl-6-octen-1-olHMDB
(R)-3,7-Dimethyloct-6-en-1-olHMDB
3,7-Dimethyl-(3R)-6-octen-1-olHMDB
3,7-Dimethyl-(R)-6-octen-1-olHMDB
Citronellol, (+-)-isomerMeSH, HMDB
CitronellolMeSH, HMDB
Citronellol, (R)-isomerMeSH, HMDB
Citronellol, (S)-isomerMeSH, HMDB
Citronellol, titanium (+4) saltMeSH, HMDB
b-CitronellolGenerator, HMDB
Β-citronellolGenerator, HMDB
(+)-(R)-CitronellolHMDB
(+)-CitronellolHMDB
(+)-β-CitronellolHMDB
(3R)-(+)-beta-CitronellolHMDB
(3R)-(+)-β-CitronellolHMDB
(3R)-3,7-Dimethyl-6-octen-1-olHMDB
(R)-(+)-3,7-Dimethyl-6-octen-1-olHMDB
(R)-(+)-β-CitronellolHMDB
(R)-CitronellolHMDB
(R)-beta-CitronellolHMDB
(R)-β-CitronellolHMDB
D-CitronellolHMDB
d-CitronellolHMDB
Chemical FormulaC10H20O
Average Molecular Weight156.2652
Monoisotopic Molecular Weight156.151415262
IUPAC Name(3R)-3,7-dimethyloct-6-en-1-ol
Traditional Nameβ-citronellol
CAS Registry Number1117-61-9
SMILES
C[C@@H](CCO)CCC=C(C)C
InChI Identifier
InChI=1S/C10H20O/c1-9(2)5-4-6-10(3)7-8-11/h5,10-11H,4,6-8H2,1-3H3/t10-/m1/s1
InChI KeyQMVPMAAFGQKVCJ-SNVBAGLBSA-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
  • Fatty alcohol
  • Fatty acyl
  • 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
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling Point221.00 to 224.00 °C. @ 760.00 mm HgThe Good Scents Company Information System
Water Solubility105.5 mg/L @ 25 °C (est)The Good Scents Company Information System
LogP3.239 (est)The Good Scents Company Information System
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility0.85 g/LALOGPS
logP3.48ALOGPS
logP2.75ChemAxon
logS-2.3ALOGPS
pKa (Strongest Acidic)17.11ChemAxon
pKa (Strongest Basic)-1.9ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area20.23 ŲChemAxon
Rotatable Bond Count5ChemAxon
Refractivity50.49 m³·mol⁻¹ChemAxon
Polarizability20.08 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+139.76731661259
DarkChem[M-H]-136.80431661259
DeepCCS[M+H]+141.62330932474
DeepCCS[M-H]-138.97930932474
DeepCCS[M-2H]-174.77230932474
DeepCCS[M+Na]+149.75830932474
AllCCS[M+H]+138.932859911
AllCCS[M+H-H2O]+134.932859911
AllCCS[M+NH4]+142.632859911
AllCCS[M+Na]+143.732859911
AllCCS[M-H]-141.532859911
AllCCS[M+Na-2H]-143.732859911
AllCCS[M+HCOO]-146.132859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
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. Predicted by Afia on May 17, 2022.5.93 minutes32390414
Predicted by Siyang on May 30, 202213.6671 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20222.84 minutes32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid24.6 seconds40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid2177.4 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid403.8 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid158.0 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid219.5 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid132.2 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid531.3 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid558.7 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)69.5 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid1131.5 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid429.2 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid1162.2 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid378.6 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid352.4 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate325.1 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA389.9 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water9.0 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
D-CitronellolC[C@@H](CCO)CCC=C(C)C1728.6Standard polar33892256
D-CitronellolC[C@@H](CCO)CCC=C(C)C1197.7Standard non polar33892256
D-CitronellolC[C@@H](CCO)CCC=C(C)C1207.7Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
D-Citronellol,1TMS,isomer #1CC(C)=CCC[C@@H](C)CCO[Si](C)(C)C1307.2Semi standard non polar33892256
D-Citronellol,1TBDMS,isomer #1CC(C)=CCC[C@@H](C)CCO[Si](C)(C)C(C)(C)C1521.8Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - D-Citronellol GC-MS (Non-derivatized) - 70eV, Positivesplash10-0296-9400000000-ba08b011d6d2fa548e822017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - D-Citronellol GC-MS (1 TMS) - 70eV, Positivesplash10-0ir0-9620000000-5dec8fa14f289a16a8b82017-10-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - D-Citronellol GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - D-Citronellol GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
MSMass Spectrum (Electron Ionization)splash10-015c-9000000000-dfb40ffb3fb172759b4f2015-03-01Not AvailableView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-Citronellol 10V, Positive-QTOFsplash10-052r-1900000000-9f559c6b6bae07c699782016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-Citronellol 20V, Positive-QTOFsplash10-052r-8900000000-f8c3d1ff7e6f87d6e43d2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-Citronellol 40V, Positive-QTOFsplash10-066u-9100000000-8ae7fa4f01b76f1eed162016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-Citronellol 10V, Negative-QTOFsplash10-0a4i-0900000000-82f8313ff8eb7c68242b2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-Citronellol 20V, Negative-QTOFsplash10-056r-0900000000-de94d5335c77bdb5afcf2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-Citronellol 40V, Negative-QTOFsplash10-0a6u-9800000000-b04acf4b20ad462747962016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-Citronellol 10V, Negative-QTOFsplash10-0a4i-0900000000-f6034c6a8245c68a37ac2021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-Citronellol 20V, Negative-QTOFsplash10-0ab9-0900000000-4432dcd3f704b4a61b302021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-Citronellol 40V, Negative-QTOFsplash10-014i-9400000000-fe45ce059cb434ed5e0c2021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-Citronellol 10V, Positive-QTOFsplash10-05o0-9200000000-e66f9e249b523e6771bb2021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-Citronellol 20V, Positive-QTOFsplash10-053r-9000000000-6e0012cc1ab177db56c02021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-Citronellol 40V, Positive-QTOFsplash10-0006-9000000000-97567d47518fef28ec282021-09-25Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView

IR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M-H]-)2023-02-04FELIX labView Spectrum
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)2023-02-04FELIX labView Spectrum
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)2023-02-04FELIX labView Spectrum
Biological Properties
Cellular Locations
  • Extracellular
  • Membrane
Biospecimen Locations
  • Feces
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected and Quantified0-17960.919 nmol/g wet fecesChildren (1-13 years old)Not Specified
Normal		 details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected and Quantified0-717668.852 nmol/g wet fecesChildren (1-13 years old)Not Specified
Treated celiac disease		 details
Associated Disorders and Diseases
Disease References
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 ]
Associated OMIM IDs
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB013722
KNApSAcK IDC00003038
Chemspider ID92127
KEGG Compound IDC09849
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkCitronellol
METLIN IDNot Available
PubChem Compound101977
PDB IDNot Available
ChEBI ID10360
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1056991
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. Turner CE, Elsohly MA, Boeren EG: Constituents of Cannabis sativa L. XVII. A review of the natural constituents. J Nat Prod. 1980 Mar-Apr;43(2):169-234. doi: 10.1021/np50008a001. [PubMed:6991645 ]
  6. Taylor WG, Schreck CE: Chiral-phase capillary gas chromatography and mosquito repellent activity of some oxazolidine derivatives of (+)- and (-)-citronellol. J Pharm Sci. 1985 May;74(5):534-9. doi: 10.1002/jps.2600740508. [PubMed:2862274 ]
  7. Santos PL, Matos JPSCF, Picot L, Almeida JRGS, Quintans JSS, Quintans-Junior LJ: Citronellol, a monoterpene alcohol with promising pharmacological activities - A systematic review. Food Chem Toxicol. 2019 Jan;123:459-469. doi: 10.1016/j.fct.2018.11.030. Epub 2018 Nov 16. [PubMed:30453001 ]
  8. Yu WN, Lai YJ, Ma JW, Ho CT, Hung SW, Chen YH, Chen CT, Kao JY, Way TD: Citronellol Induces Necroptosis of Human Lung Cancer Cells via TNF-alpha Pathway and Reactive Oxygen Species Accumulation. In Vivo. 2019 Jul-Aug;33(4):1193-1201. doi: 10.21873/invivo.11590. [PubMed:31280209 ]
  9. Rajendran J, Pachaiappan P, Subramaniyan S: Dose-dependent chemopreventive effects of citronellol in DMBA-induced breast cancer among rats. Drug Dev Res. 2019 Sep;80(6):867-876. doi: 10.1002/ddr.21570. Epub 2019 Jul 16. [PubMed:31313341 ]
  10. Silva D, Diniz-Neto H, Cordeiro L, Silva-Neta M, Silva S, Andrade-Junior F, Leite M, Nobrega J, Morais M, Souza J, Rosa L, Melo T, Souza H, Sousa A, Rodrigues G, Oliveira-Filho A, Lima E: (R)-(+)-beta-Citronellol and (S)-(-)-beta-Citronellol in Combination with Amphotericin B against Candida Spp. Int J Mol Sci. 2020 Mar 5;21(5). pii: ijms21051785. doi: 10.3390/ijms21051785. [PubMed:32150884 ]
  11. Ribeiro-Filho HV, de Souza Silva CM, de Siqueira RJ, Lahlou S, dos Santos AA, Magalhaes PJ: Biphasic cardiovascular and respiratory effects induced by beta-citronellol. Eur J Pharmacol. 2016 Mar 15;775:96-105. doi: 10.1016/j.ejphar.2016.02.025. Epub 2016 Feb 9. [PubMed:26872991 ]
  12. (). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .
  13. Gunstone, Frank D., John L. Harwood, and Albert J. Dijkstra (2007). The lipid handbook with CD-ROM. CRC Press.