Showing NP-Card for (-)-citronellol (NP0239293)

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Record Information
Version2.0
Created at2022-09-06 22:51:39 UTC
Updated at2022-09-06 22:51:39 UTC
NP-MRD IDNP0239293
Secondary Accession NumbersNone
Natural Product Identification
Common Name(-)-citronellol
DescriptionL-Citronellol, also known as (S)-β-citronellol, belongs to the class of organic compounds known as acyclic monoterpenoids. These are monoterpenes that do not contain a cycle. Thus, L-citronellol is considered to be an isoprenoid lipid molecule. L-Citronellol is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral. L-Citronellol exists in all living organisms, ranging from bacteria to humans. L-Citronellol is a floral, geranium, and oil tasting compound. Outside of the human body, L-Citronellol has been detected, but not quantified in, herbs and spices. This could make L-citronellol a potential biomarker for the consumption of these foods. L-Citronellol, with regard to humans, has been linked to the inborn metabolic disorder celiac disease. (-)-citronellol is found in Acokanthera oblongifolia, Callitropsis nootkatensis, Centaurea benedicta, Chamaecyparis lawsoniana, Chamaecyparis obtusa, Citrus aurantium, Citrus unshiu, Citrus wilsonii, Croton malambo, Eremothecium ashbyi, Oenanthe aquatica and Rosa gallica. A citronellol that is oct-6-ene substituted by a hydroxy group at position 1 and methyl groups at positions 3 and 7 (the 3S-enantiomer).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0239293 ((-)-citronellol)

  Mrv1652309272007402D          

 11 10  0  0  0  0            999 V2000
10001.371210000.4542    0.0000 C   0  0  1  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  6  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
Download

3D MOL for NP0239293 ((-)-citronellol)

     RDKit          3D

 31 30  0  0  0  0  0  0  0  0999 V2000
   -3.5354   -0.6500   -1.8009 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7781    0.2023   -0.8611 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4928    0.7895    0.2919 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4824    0.4152   -1.0782 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7107    1.2524   -0.1667 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3425    0.6123    0.6447 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4378   -0.0658   -0.0873 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.0725   -1.2151   -0.9429 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6326   -0.3609    0.8287 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8231   -0.6800   -0.0346 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0359    0.4642   -0.8322 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8992   -1.1147   -2.5812 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9713   -1.5164   -1.2283 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3750   -0.1058   -2.2951 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5119    1.8973    0.2714 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9094    0.4877    1.2109 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5046    0.3928    0.4238 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9959   -0.0161   -1.9696 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2561    2.1152   -0.7698 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4269    1.7319    0.5709 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1143   -0.1888    1.3201 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8233    1.3365    1.3654 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8557    0.7404   -0.7957 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0423   -1.5518   -0.6499 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1208   -0.9663   -1.9982 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7817   -2.0628   -0.7424 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8389    0.4980    1.4789 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3989   -1.2557    1.4690 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6715   -1.5622   -0.6475 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7299   -0.8313    0.6012 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3566    1.2082   -0.2543 H   0  0  0  0  0  0  0  0  0  0  0  0
  8  7  1  0
  7  9  1  0
  9 10  1  0
 10 11  1  0
  7  6  1  0
  6  5  1  0
  5  4  1  0
  4  2  2  3
  2  1  1  0
  2  3  1  0
  8 24  1  0
  8 25  1  0
  8 26  1  0
  7 23  1  6
  9 27  1  0
  9 28  1  0
 10 29  1  0
 10 30  1  0
 11 31  1  0
  6 21  1  0
  6 22  1  0
  5 19  1  0
  5 20  1  0
  4 18  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
M  END
Download

3D SDF for NP0239293 ((-)-citronellol)

  Mrv1652309272007402D          

 11 10  0  0  0  0            999 V2000
10001.371210000.4542    0.0000 C   0  0  1  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  6  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>
NP0239293

> <DATABASE_NAME>
NP-MRD

> <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-/m0/s1

> <INCHI_KEY>
QMVPMAAFGQKVCJ-JTQLQIEISA-N

> <FORMULA>
C10H20O

> <MOLECULAR_WEIGHT>
156.269

> <EXACT_MASS>
156.151415264

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
31

> <JCHEM_AVERAGE_POLARIZABILITY>
20.098591710228593

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3S)-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>
(-)-citronellol

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for NP0239293 ((-)-citronellol)

Download
PDB for NP0239293 ((-)-citronellol)
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    8669.2268667.514   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    8666.5568667.514   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    8663.8898667.514   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    8671.8928667.514   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

Download
3D PDB for NP0239293 ((-)-citronellol)
Download
SMILES for NP0239293 ((-)-citronellol)
C[C@H](CCO)CCC=C(C)C
Download
INCHI for NP0239293 ((-)-citronellol)
InChI=1S/C10H20O/c1-9(2)5-4-6-10(3)7-8-11/h5,10-11H,4,6-8H2,1-3H3/t10-/m0/s1
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View in JSmol
Synonyms
Chemical FormulaC10H20O
Average Mass156.2690 Da
Monoisotopic Mass156.15142 Da
IUPAC Name(3S)-3,7-dimethyloct-6-en-1-ol
Traditional Name(-)-citronellol
CAS Registry NumberNot Available
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-/m0/s1
InChI KeyQMVPMAAFGQKVCJ-JTQLQIEISA-N
Experimental Spectra
Not Available
Predicted Spectra
Chemical Shift Submissions
Not Available
Species
Species of Origin
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
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
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
Polarizability20.1 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0035094  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB013723  
KNApSAcK IDC00000844  
Chemspider IDNot Available
KEGG Compound IDC11386  
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkCitronellol  
METLIN IDNot Available
PubChem Compound7793  
PDB IDNot Available
ChEBI ID88  
Good Scents IDNot Available
References
General References
  1. LOTUS database [Link]