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Showing NP-Card for (S)-Ipsdienol (NP0045064)

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Record Information
Version2.0
Created at2022-03-10 18:57:21 UTC
Updated at2022-03-10 22:16:36 UTC
NP-MRD IDNP0045064
Secondary Accession NumbersNone
Natural Product Identification
Common Name(S)-Ipsdienol
DescriptionIpsdienol or S-ipsdienol belongs to the class of organic compounds known as acyclic monoterpenoids. These are monoterpenes that do not contain a cycle. Monoterpenoids are terpenes that contain 10 carbon atoms and are comprised of two isoprene units. The biosynthesis of monoterpenes is known to occur mainly through the methyl-eritritol-phosphate (MEP) pathway in the plastids. S-ipsdienol is considered to be an isoprenoid lipid molecule. S-ipsdienol is a secondary alcohol and it is very hydrophobic, practically insoluble in water but soluble in organic solvents such as methanol, ethanol and ethyl acetate. Ipsdienol was first identified from the bark beetle Ips confusus, in which it is believed to be a main sex attractant (DOI: 10.1126/Science.154.3748.509). It is also one of the major aggregation pheromones of the bark beetle (PMID: 20727970 ). Ipsdienol has also been identified in a number of plant species, including Cannabis sativa (PMID: 8984153 ).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0045064 ((S)-Ipsdienol)


  Mrv1652303192001383D          

 11 10  0  0  0  0            999 V2000
    2.6291    0.1519   -1.0611 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2088    1.7668    0.5529 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1280    1.8672   -0.8596 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2866   -2.4216    1.4227 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8242   -0.9222   -0.3439 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6169   -0.0775    0.5991 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7795   -0.5149    1.1016 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9224    1.0948    0.1089 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9624   -1.3109    0.7309 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4089   -0.8644    0.2735 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.1735   -1.0428   -1.0723 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  5  2  0  0  0  0
  2  8  1  0  0  0  0
  3  8  1  0  0  0  0
  4  9  2  0  0  0  0
  5  9  1  0  0  0  0
  6  8  2  3  0  0  0
  6 10  1  0  0  0  0
  7  9  1  0  0  0  0
  7 10  1  0  0  0  0
 10 11  1  6  0  0  0
M  END
Download

3D MOL for NP0045064 ((S)-Ipsdienol)

     RDKit          3D

 27 26  0  0  0  0  0  0  0  0999 V2000
    3.2510    1.7567   -0.0690 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4031    0.4728    0.1200 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2546   -0.4072    0.0023 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4358   -1.7120    0.1996 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9467    0.1743   -0.3277 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1638   -0.8154   -0.4316 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0856   -1.6618   -1.5202 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4254   -0.0746   -0.7694 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3412    0.1581    0.1519 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5811    0.8957   -0.2163 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1977   -0.2844    1.5605 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2914    2.1669   -0.3091 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0948    2.4102    0.0167 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3923    0.0657    0.3657 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5921   -2.3640    0.1139 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3936   -2.1409    0.4416 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0547    0.6566   -1.3375 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7531    0.9982    0.3740 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3427   -1.4095    0.4661 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1674   -1.2094   -2.3767 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5611    0.2611   -1.7851 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5592    1.8874    0.2854 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6848    0.9863   -1.3211 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4788    0.3759    0.1528 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1492   -0.2232    1.9165 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5106   -1.3470    1.6213 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7857    0.3835    2.2213 H   0  0  0  0  0  0  0  0  0  0  0  0
 10  9  1  0
  9 11  1  0
  9  8  2  3
  8  6  1  0
  6  7  1  0
  6  5  1  0
  5  3  1  0
  3  4  2  3
  3  2  1  0
  2  1  2  3
 10 22  1  0
 10 23  1  0
 10 24  1  0
 11 25  1  0
 11 26  1  0
 11 27  1  0
  8 21  1  0
  6 19  1  1
  7 20  1  0
  5 17  1  0
  5 18  1  0
  4 15  1  0
  4 16  1  0
  2 14  1  0
  1 12  1  0
  1 13  1  0
M  END
Download

3D SDF for NP0045064 ((S)-Ipsdienol)


  Mrv1652303192001383D          

 11 10  0  0  0  0            999 V2000
    2.6291    0.1519   -1.0611 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2088    1.7668    0.5529 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1280    1.8672   -0.8596 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2866   -2.4216    1.4227 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8242   -0.9222   -0.3439 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6169   -0.0775    0.5991 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7795   -0.5149    1.1016 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9224    1.0948    0.1089 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9624   -1.3109    0.7309 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4089   -0.8644    0.2735 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.1735   -1.0428   -1.0723 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  5  2  0  0  0  0
  2  8  1  0  0  0  0
  3  8  1  0  0  0  0
  4  9  2  0  0  0  0
  5  9  1  0  0  0  0
  6  8  2  3  0  0  0
  6 10  1  0  0  0  0
  7  9  1  0  0  0  0
  7 10  1  0  0  0  0
 10 11  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0045064

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C10H16O/c1-5-9(4)7-10(11)6-8(2)3/h5-6,10-11H,1,4,7H2,2-3H3/t10-/m1/s1

> <INCHI_KEY>
NHMKYUHMPXBMFI-SNVBAGLBSA-N

> <FORMULA>
C10H16O

> <MOLECULAR_WEIGHT>
152.237

> <EXACT_MASS>
152.120115135

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
27

> <JCHEM_AVERAGE_POLARIZABILITY>
18.36951808454913

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(4S)-2-methyl-6-methylideneocta-2,7-dien-4-ol

> <ALOGPS_LOGP>
2.56

> <JCHEM_LOGP>
2.3062890696666667

> <ALOGPS_LOGS>
-2.23

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
18.331069717818597

> <JCHEM_PKA_STRONGEST_BASIC>
-1.3417901054261456

> <JCHEM_POLAR_SURFACE_AREA>
20.23

> <JCHEM_REFRACTIVITY>
49.8945

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
9.00e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(4S)-2-methyl-6-methylideneocta-2,7-dien-4-ol

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for NP0045064 ((S)-Ipsdienol)

Download
PDB for NP0045064 ((S)-Ipsdienol)
HEADER    PROTEIN                                 19-MAR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   19-MAR-20         0                                  
HETATM    1  C   UNK     0       2.629   0.152  -1.061  0.00  0.00           C+0
HETATM    2  C   UNK     0      -3.209   1.767   0.553  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.128   1.867  -0.860  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.287  -2.422   1.423  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.824  -0.922  -0.344  0.00  0.00           C+0
HETATM    6  C   UNK     0      -1.617  -0.078   0.599  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.780  -0.515   1.102  0.00  0.00           C+0
HETATM    8  C   UNK     0      -1.922   1.095   0.109  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.962  -1.311   0.731  0.00  0.00           C+0
HETATM   10  C   UNK     0      -0.409  -0.864   0.274  0.00  0.00           C+0
HETATM   11  O   UNK     0      -0.174  -1.043  -1.072  0.00  0.00           O+0
CONECT    1    5                                                            
CONECT    2    8                                                            
CONECT    3    8                                                            
CONECT    4    9                                                            
CONECT    5    1    9                                                       
CONECT    6    8   10                                                       
CONECT    7    9   10                                                       
CONECT    8    2    3    6                                                  
CONECT    9    4    5    7                                                  
CONECT   10    6    7   11                                                  
CONECT   11   10                                                            
MASTER        0    0    0    0    0    0    0    0   11    0   20    0
END

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3D PDB for NP0045064 ((S)-Ipsdienol)
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SMILES for NP0045064 ((S)-Ipsdienol)
CC(C)=C[C@@H](O)CC(=C)C=C
Download
INCHI for NP0045064 ((S)-Ipsdienol)
InChI=1S/C10H16O/c1-5-9(4)7-10(11)6-8(2)3/h5-6,10-11H,1,4,7H2,2-3H3/t10-/m1/s1
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View in JSmol
Synonyms
ValueSource
IpsdienolMeSH
2-Methyl-6-methylene-2,7-octadien-4-olMeSH
Chemical FormulaC10H16O
Average Mass152.2370 Da
Monoisotopic Mass152.12012 Da
IUPAC Name(4S)-2-methyl-6-methylideneocta-2,7-dien-4-ol
Traditional Name(4S)-2-methyl-6-methylideneocta-2,7-dien-4-ol
CAS Registry Number13040-13-6
SMILES
CC(C)=C[C@@H](O)CC(=C)C=C
InChI Identifier
InChI=1S/C10H16O/c1-5-9(4)7-10(11)6-8(2)3/h5-6,10-11H,1,4,7H2,2-3H3/t10-/m1/s1
InChI KeyNHMKYUHMPXBMFI-SNVBAGLBSA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Cannabis sativaNULL
      Not Available
Curcuma manggaPlant
Ips cembraeLOTUS Database
Ips paraconfususLOTUS Database
Laurus nobilisLOTUS Database
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
    • 

  • Secondary alcohol
    • 

  • Organic oxygen compound
    • 

  • Hydrocarbon derivative
    • 

  • 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
logP2.56ALOGPS
logP2.31ChemAxon
logS-2.2ALOGPS
pKa (Strongest Acidic)18.33ChemAxon
pKa (Strongest Basic)-1.3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area20.23 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity49.89 m³·mol⁻¹ChemAxon
Polarizability18.37 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia Link(S)-Ipsdienol  
METLIN IDNot Available
PubChem Compound92301  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Blomquist GJ, Figueroa-Teran R, Aw M, Song M, Gorzalski A, Abbott NL, Chang E, Tittiger C: Pheromone production in bark beetles. Insect Biochem Mol Biol. 2010 Oct;40(10):699-712. doi: 10.1016/j.ibmb.2010.07.013. Epub 2010 Aug 19. [PubMed:20727970  ]