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Showing NP-Card for (R)-Citronellal (NP0048337)

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Record Information
Version2.0
Created at2022-03-17 20:54:51 UTC
Updated at2022-03-17 20:54:51 UTC
NP-MRD IDNP0048337
Secondary Accession NumbersNone
Natural Product Identification
Common Name(R)-Citronellal
Description(R)-Citronellal belongs to the class of organic compounds known as acyclic monoterpenoids. These are monoterpenes that do not contain a cycle. Thus, (R)-citronellal is considered to be an isoprenoid lipid molecule (R)-Citronellal is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral (R)-Citronellal exists in all living organisms, ranging from bacteria to humans (R)-Citronellal is a citrus, fresh, and herbal tasting compound. Outside of the human body, (R)-Citronellal is found, on average, in the highest concentration within lemon balms (R)-Citronellal has also been detected, but not quantified in, citrus and herbs and spices. This could make (R)-citronellal a potential biomarker for the consumption of these foods. (R)-Citronellal is found in Aloysia triphylla, Backhousia citriodora, Centaurea benedicta, Citrus junos, Citrus limon, Citrus limonia, Citrus spp., Citrus wilsonii, Cymbopogon nardus , Eucalyptus citriodora , Juniperus communis, Litsea cubeba, Ocimum gratissimum and Phlebalium nudum. (R)-Citronellal was first documented in 2005 (PMID: 15890377). The (3R)-stereoisomer of 3,7-dimethyloct-6-enal (citronellal) (PMID: 18436619) (PMID: 16419049) (PMID: 17081038) (PMID: 16904803).
Structure
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MOLSDFPDBSMILESInChI

MOL for NP0048337 ((R)-Citronellal)


  Mrv1652309272007402D          

 11 10  0  0  0  0            999 V2000
10000.651210000.4542    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
10001.366310000.0428    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10002.079510000.4542    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10002.794610000.0428    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10003.507810000.4542    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10004.222910000.0428    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10003.507810001.2792    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.936610000.0428    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.222410000.4542    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.507810000.0428    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10000.651210001.2792    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  2  0  0  0  0
M  END
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3D MOL for NP0048337 ((R)-Citronellal)

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3D SDF for NP0048337 ((R)-Citronellal)

  Mrv1652309272007402D          

 11 10  0  0  0  0            999 V2000
10000.651210000.4542    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
10001.366310000.0428    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10002.079510000.4542    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10002.794610000.0428    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10003.507810000.4542    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10004.222910000.0428    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10003.507810001.2792    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.936610000.0428    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.222410000.4542    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.507810000.0428    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10000.651210001.2792    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  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0048337

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C10H18O/c1-9(2)5-4-6-10(3)7-8-11/h5,8,10H,4,6-7H2,1-3H3/t10-/m1/s1

> <INCHI_KEY>
NEHNMFOYXAPHSD-SNVBAGLBSA-N

> <FORMULA>
C10H18O

> <MOLECULAR_WEIGHT>
154.2493

> <EXACT_MASS>
154.135765198

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
29

> <JCHEM_AVERAGE_POLARIZABILITY>
19.17573127849107

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3R)-3,7-dimethyloct-6-enal

> <ALOGPS_LOGP>
3.25

> <JCHEM_LOGP>
2.709875916666667

> <ALOGPS_LOGS>
-2.63

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
18.324015468474656

> <JCHEM_PKA_STRONGEST_BASIC>
-6.9503143064911965

> <JCHEM_POLAR_SURFACE_AREA>
17.07

> <JCHEM_REFRACTIVITY>
49.297399999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.59e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(R)-(+)-citronellal

> <JCHEM_VEBER_RULE>
1

$$$$

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3D-SDF for NP0048337 ((R)-Citronellal)
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PDB for NP0048337 ((R)-Citronellal)
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    8667.8828667.514   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0    8669.2178666.747   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0    8670.5488667.514   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0    8671.8838666.747   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0    8673.2148667.514   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0    8674.5498666.747   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0    8673.2148669.055   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0    8666.5488666.747   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0    8665.2158667.514   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0    8663.8818666.747   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0    8667.8828669.055   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 NP0048337 ((R)-Citronellal)
Download
SMILES for NP0048337 ((R)-Citronellal)
C[C@H](CCC=C(C)C)CC=O
Download
INCHI for NP0048337 ((R)-Citronellal)
InChI=1S/C10H18O/c1-9(2)5-4-6-10(3)7-8-11/h5,8,10H,4,6-7H2,1-3H3/t10-/m1/s1
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View in JSmol
Synonyms
ValueSource
(3R)-(+)-CitronellalChEBI
(3R)-3,7-Dimethyl-6-octenalChEBI
(R)-3,7-Dimethyl-6-octenalChEBI
(R)-3,7-Dimethyloct-6-enalChEBI
(+)-CitronellalHMDB
(3R)-3,7-Dimethyloct-6-enalHMDB
(R)-(+)-CitronellalHMDB
3,7-Dimethyl-(3R)-6-octenalHMDB
(R)-CitronellalPhytoBank
d-CitronellalPhytoBank
3,7-Dimethyl-6-octenalPhytoBank
(±)-CitronellalPhytoBank
2,3-DihydrocitralPhytoBank
2,6-Dimethylhept-5-enecarboxaldehydePhytoBank
3,7-Dimethyloct-6-en-1-alPhytoBank
RhodinalPhytoBank
dl-CitronellalPhytoBank
beta-CitronellalPhytoBank
β-CitronellalPhytoBank
Chemical FormulaC10H18O
Average Mass154.2493 Da
Monoisotopic Mass154.13577 Da
IUPAC Name(3R)-3,7-dimethyloct-6-enal
Traditional Name(R)-(+)-citronellal
CAS Registry Number2385-77-5
SMILES
C[C@H](CCC=C(C)C)CC=O
InChI Identifier
InChI=1S/C10H18O/c1-9(2)5-4-6-10(3)7-8-11/h5,8,10H,4,6-7H2,1-3H3/t10-/m1/s1
InChI KeyNEHNMFOYXAPHSD-SNVBAGLBSA-N
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Aloysia triphyllaLOTUS Database
Backhousia citriodoraLOTUS Database
Centaurea benedictaLOTUS Database
Citrus junosLOTUS Database
Citrus limonLOTUS Database
Citrus limoniaLOTUS Database
Citrus spp.Plant
Citrus wilsoniiLOTUS Database
Cymbopogon nardusPlant
Eucalyptus citriodoraPlant
Juniperus communisLOTUS Database
Litsea cubebaLOTUS Database
Melissa officinalis L.FooDB
Ocimum gratissimumPlant
Phlebalium nudum-
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
    • 

  • Medium-chain aldehyde
    • 

  • Alpha-hydrogen aldehyde
    • 

  • Organic oxygen compound
    • 

  • Organic oxide
    • 

  • Hydrocarbon derivative
    • 

  • Organooxygen compound
    • 

  • Carbonyl group
    • 

  • Aldehyde
    • 

  • 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
logP3.25ALOGPS
logP2.71ChemAxon
logS-2.6ALOGPS
pKa (Strongest Acidic)18.32ChemAxon
pKa (Strongest Basic)-7ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area17.07 ŲChemAxon
Rotatable Bond Count5ChemAxon
Refractivity49.3 m³·mol⁻¹ChemAxon
Polarizability19.18 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0035820  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB014582  
KNApSAcK IDC00003037  
Chemspider ID67959  
KEGG Compound IDC09848  
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound75427  
PDB IDNot Available
ChEBI ID299  
Good Scents IDNot Available
References
General References
  1. Yoshida N, Takada T, Yamamura Y, Adachi I, Suzuki H, Kawakami J: Inhibitory effects of terpenoids on multidrug resistance-associated protein 2- and breast cancer resistance protein-mediated transport. Drug Metab Dispos. 2008 Jul;36(7):1206-11. doi: 10.1124/dmd.107.019513. Epub 2008 Apr 24. [PubMed:18436619  ] 
  2. Yoshida N, Takagi A, Kitazawa H, Kawakami J, Adachi I: Effects of citronellal, a monoterpenoid in Zanthoxyli Fructus, on the intestinal absorption of digoxin in vitro and in vivo. J Pharm Sci. 2006 Mar;95(3):552-60. doi: 10.1002/jps.20563. [PubMed:16419049  ] 
  3. Chavan SP, Thakkar M, Jogdand GF, Kalkote UR: First enantiospecific synthesis of (-)-parvifoline and (-)-curcuquinone. J Org Chem. 2006 Nov 10;71(23):8986-8. doi: 10.1021/jo061730d. [PubMed:17081038  ] 
  4. Yoshida N, Koizumi M, Adachi I, Kawakami J: Inhibition of P-glycoprotein-mediated transport by terpenoids contained in herbal medicines and natural products. Food Chem Toxicol. 2006 Dec;44(12):2033-9. doi: 10.1016/j.fct.2006.07.003. Epub 2006 Jul 10. [PubMed:16904803  ] 
  5. Yoshida N, Takagi A, Kitazawa H, Kawakami J, Adachi I: Inhibition of P-glycoprotein-mediated transport by extracts of and monoterpenoids contained in Zanthoxyli fructus. Toxicol Appl Pharmacol. 2005 Dec 1;209(2):167-73. doi: 10.1016/j.taap.2005.04.001. [PubMed:15890377  ]