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Showing NP-Card for Cymbopogonol (NP0048637)

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Record Information
Version2.0
Created at2022-03-17 20:59:45 UTC
Updated at2022-03-17 20:59:45 UTC
NP-MRD IDNP0048637
Secondary Accession NumbersNone
Natural Product Identification
Common NameCymbopogonol
DescriptionCymbopogonol belongs to the class of organic compounds known as colensane and clerodane diterpenoids. These are diterpenoids with a structure based on the clerodane or the colensane skeleton. Clerodanes arise from labdanes by two methyl migrations. Cymbopogonol is an extremely weak basic (essentially neutral) compound (based on its pKa). Outside of the human body, cymbopogonol is found, on average, in the highest concentration in lemon grass. Cymbopogonol has also been detected, but not quantified in, herbs and spices. This could make cymbopogonol a potential biomarker for the consumption of these foods.
Structure
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MOLSDFPDBSMILESInChI

MOL for NP0048637 (Cymbopogonol)


  Mrv0541 05061309242D          

 31 35  0  0  0  0            999 V2000
    2.5200    1.3518    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9130    1.0335    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.4112   -2.1393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5652   -2.0033    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.5863   -2.1267    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3815    0.0353    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1116   -2.0891    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9068    0.0729    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.0313    0.0102    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2064    0.0227    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1822   -0.3378    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9365   -2.1016    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2559   -1.1595    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7614   -2.1142    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4618   -2.0640    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5566    0.0478    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2867   -2.0765    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7317    0.0604    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1246    0.7905    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.0096   -1.4186    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9409   -0.0138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.4329   -0.7105    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7831   -0.6854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5349   -1.3810    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4835   -0.6352    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0602   -1.3433    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1847   -1.4061    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9582   -0.6728    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7100   -1.3684    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3084   -0.6478    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.2578   -0.7230    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 10  9  1  0  0  0  0
 13 11  1  0  0  0  0
 14 12  1  0  0  0  0
 17 15  1  0  0  0  0
 18 16  1  0  0  0  0
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 21 11  1  0  0  0  0
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 25 21  1  0  0  0  0
 26  4  1  0  0  0  0
 26 13  1  0  0  0  0
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 27  5  1  0  0  0  0
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 28  6  1  0  0  0  0
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 28 23  1  0  0  0  0
 28 24  1  0  0  0  0
 29  7  1  0  0  0  0
 29 17  1  0  0  0  0
 29 24  1  0  0  0  0
 30  8  1  0  0  0  0
 30 18  1  0  0  0  0
 30 25  1  0  0  0  0
 30 29  1  0  0  0  0
 31 22  1  0  0  0  0
M  END
Download

3D MOL for NP0048637 (Cymbopogonol)

Download
3D SDF for NP0048637 (Cymbopogonol)

  Mrv0541 05061309242D          

 31 35  0  0  0  0            999 V2000
    2.5200    1.3518    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9130    1.0335    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.4112   -2.1393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5652   -2.0033    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.5863   -2.1267    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3815    0.0353    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1116   -2.0891    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9068    0.0729    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.0313    0.0102    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2064    0.0227    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1822   -0.3378    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9365   -2.1016    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2559   -1.1595    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7614   -2.1142    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4618   -2.0640    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5566    0.0478    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2867   -2.0765    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7317    0.0604    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1246    0.7905    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.0096   -1.4186    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9409   -0.0138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.4329   -0.7105    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7831   -0.6854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5349   -1.3810    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4835   -0.6352    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0602   -1.3433    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1847   -1.4061    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9582   -0.6728    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7100   -1.3684    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3084   -0.6478    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.2578   -0.7230    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 10  9  1  0  0  0  0
 13 11  1  0  0  0  0
 14 12  1  0  0  0  0
 17 15  1  0  0  0  0
 18 16  1  0  0  0  0
 19  1  1  0  0  0  0
 19  2  1  0  0  0  0
 20  3  2  0  0  0  0
 21 11  1  0  0  0  0
 21 19  1  0  0  0  0
 22  9  1  0  0  0  0
 22 20  1  0  0  0  0
 23 10  1  0  0  0  0
 24 12  1  0  0  0  0
 25 21  1  0  0  0  0
 26  4  1  0  0  0  0
 26 13  1  0  0  0  0
 26 15  1  0  0  0  0
 26 25  1  0  0  0  0
 27  5  1  0  0  0  0
 27 14  1  0  0  0  0
 27 20  1  0  0  0  0
 27 23  1  0  0  0  0
 28  6  1  0  0  0  0
 28 16  1  0  0  0  0
 28 23  1  0  0  0  0
 28 24  1  0  0  0  0
 29  7  1  0  0  0  0
 29 17  1  0  0  0  0
 29 24  1  0  0  0  0
 30  8  1  0  0  0  0
 30 18  1  0  0  0  0
 30 25  1  0  0  0  0
 30 29  1  0  0  0  0
 31 22  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0048637

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)C1CCC2(C)CCC3(C)C4CCC5(C)C(CCC(O)C5=C)C4(C)CCC3(C)C12

> <INCHI_IDENTIFIER>
InChI=1S/C30H50O/c1-19(2)21-11-13-26(4)15-17-29(7)24-12-14-27(5)20(3)22(31)9-10-23(27)28(24,6)16-18-30(29,8)25(21)26/h19,21-25,31H,3,9-18H2,1-2,4-8H3

> <INCHI_KEY>
QEDMSLJZGCZBIF-UHFFFAOYSA-N

> <FORMULA>
C30H50O

> <MOLECULAR_WEIGHT>
426.7174

> <EXACT_MASS>
426.386166222

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_AVERAGE_POLARIZABILITY>
53.83680177506889

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2,5,10,13,19-pentamethyl-18-methylidene-8-(propan-2-yl)pentacyclo[11.8.0.0²,¹⁰.0⁵,⁹.0¹⁴,¹⁹]henicosan-17-ol

> <ALOGPS_LOGP>
6.11

> <JCHEM_LOGP>
7.448046480999999

> <ALOGPS_LOGS>
-6.44

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
18.418883509953552

> <JCHEM_PKA_STRONGEST_BASIC>
-1.3033803527463164

> <JCHEM_POLAR_SURFACE_AREA>
20.23

> <JCHEM_REFRACTIVITY>
130.90829999999994

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.55e-04 g/l

> <JCHEM_TRADITIONAL_IUPAC>
8-isopropyl-2,5,10,13,19-pentamethyl-18-methylidenepentacyclo[11.8.0.0²,¹⁰.0⁵,⁹.0¹⁴,¹⁹]henicosan-17-ol

> <JCHEM_VEBER_RULE>
1

$$$$

Download
3D-SDF for NP0048637 (Cymbopogonol)
Download
PDB for NP0048637 (Cymbopogonol)
HEADER    PROTEIN                                 06-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAY-13         0                                  
HETATM    1  C   UNK     0       4.704   2.523   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       7.304   1.929   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      15.701  -3.993   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.788  -3.739   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      14.161  -3.970   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      11.912   0.066   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       9.542  -3.900   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       7.293   0.136   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      14.992   0.019   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      13.452   0.042   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.073  -0.631   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      11.081  -3.923   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       4.211  -2.164   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      12.621  -3.947   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       6.462  -3.853   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      10.372   0.089   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       8.002  -3.876   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       8.833   0.113   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       5.833   1.476   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      14.951  -2.648   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       5.490  -0.026   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      15.741  -1.326   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      12.662  -1.279   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      10.332  -2.578   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       6.503  -1.186   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       5.712  -2.507   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      13.411  -2.625   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      11.122  -1.256   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       8.792  -2.554   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       8.042  -1.209   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0      17.281  -1.350   0.000  0.00  0.00           O+0
CONECT    1   19                                                            
CONECT    2   19                                                            
CONECT    3   20                                                            
CONECT    4   26                                                            
CONECT    5   27                                                            
CONECT    6   28                                                            
CONECT    7   29                                                            
CONECT    8   30                                                            
CONECT    9   10   22                                                       
CONECT   10    9   23                                                       
CONECT   11   13   21                                                       
CONECT   12   14   24                                                       
CONECT   13   11   26                                                       
CONECT   14   12   27                                                       
CONECT   15   17   26                                                       
CONECT   16   18   28                                                       
CONECT   17   15   29                                                       
CONECT   18   16   30                                                       
CONECT   19    1    2   21                                                  
CONECT   20    3   22   27                                                  
CONECT   21   11   19   25                                                  
CONECT   22    9   20   31                                                  
CONECT   23   10   27   28                                                  
CONECT   24   12   28   29                                                  
CONECT   25   21   26   30                                                  
CONECT   26    4   13   15   25                                             
CONECT   27    5   14   20   23                                             
CONECT   28    6   16   23   24                                             
CONECT   29    7   17   24   30                                             
CONECT   30    8   18   25   29                                             
CONECT   31   22                                                            
MASTER        0    0    0    0    0    0    0    0   31    0   70    0
END

Download
3D PDB for NP0048637 (Cymbopogonol)
Download
SMILES for NP0048637 (Cymbopogonol)
CC(C)C1CCC2(C)CCC3(C)C4CCC5(C)C(CCC(O)C5=C)C4(C)CCC3(C)C12
Download
INCHI for NP0048637 (Cymbopogonol)
InChI=1S/C30H50O/c1-19(2)21-11-13-26(4)15-17-29(7)24-12-14-27(5)20(3)22(31)9-10-23(27)28(24,6)16-18-30(29,8)25(21)26/h19,21-25,31H,3,9-18H2,1-2,4-8H3
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View in JSmol
Synonyms
ValueSource
D:A-friedo-4(23)-lupen-3b-olHMDB
Chemical FormulaC30H50O
Average Mass426.7174 Da
Monoisotopic Mass426.38617 Da
IUPAC Name2,5,10,13,19-pentamethyl-18-methylidene-8-(propan-2-yl)pentacyclo[11.8.0.0²,¹⁰.0⁵,⁹.0¹⁴,¹⁹]henicosan-17-ol
Traditional Name8-isopropyl-2,5,10,13,19-pentamethyl-18-methylidenepentacyclo[11.8.0.0²,¹⁰.0⁵,⁹.0¹⁴,¹⁹]henicosan-17-ol
CAS Registry Number60816-94-6
SMILES
CC(C)C1CCC2(C)CCC3(C)C4CCC5(C)C(CCC(O)C5=C)C4(C)CCC3(C)C12
InChI Identifier
InChI=1S/C30H50O/c1-19(2)21-11-13-26(4)15-17-29(7)24-12-14-27(5)20(3)22(31)9-10-23(27)28(24,6)16-18-30(29,8)25(21)26/h19,21-25,31H,3,9-18H2,1-2,4-8H3
InChI KeyQEDMSLJZGCZBIF-UHFFFAOYSA-N
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Cymbopogon citratusFooDB
Chemical Taxonomy
Description Belongs to the class of organic compounds known as colensane and clerodane diterpenoids. These are diterpenoids with a structure based on the clerodane or the colensane skeleton. Clerodanes arise from labdanes by two methyl migrations.
KingdomOrganic compounds  
Super ClassLipids and lipid-like molecules  
ClassPrenol lipids  
Sub ClassDiterpenoids  
Direct ParentColensane and clerodane diterpenoids  
Alternative Parents
Substituents
  • Clerodane diterpenoid
    • 

  • Steroid
    • 

  • Cyclic alcohol
    • 

  • Secondary alcohol
    • 

  • Organic oxygen compound
    • 

  • Hydrocarbon derivative
    • 

  • Organooxygen compound
    • 

  • Alcohol
    • 

  • Aliphatic homopolycyclic compound
Molecular FrameworkAliphatic homopolycyclic compounds
External DescriptorsNot Available
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
logP6.11ALOGPS
logP7.45ChemAxon
logS-6.4ALOGPS
pKa (Strongest Acidic)18.42ChemAxon
pKa (Strongest Basic)-1.3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area20.23 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity130.91 m³·mol⁻¹ChemAxon
Polarizability53.84 ųChemAxon
Number of Rings5ChemAxon
BioavailabilityYesChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0036904  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB015867  
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound131752084  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References