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Showing NP-Card for Litseacubebic acid (NP0086473)

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Record Information
Version2.0
Created at2022-04-29 06:46:02 UTC
Updated at2022-04-29 06:46:02 UTC
NP-MRD IDNP0086473
Secondary Accession NumbersNone
Natural Product Identification
Common NameLitseacubebic acid
DescriptionLITSEACUBEBIC ACID, also known as litseacubebate, belongs to the class of organic compounds known as medium-chain hydroxy acids and derivatives. These are hydroxy acids with a 6 to 12 carbon atoms long side chain. Litseacubebic acid is found in Litsea cubeba . Litseacubebic acid was first documented in 2010 (PMID: 20944522). Based on a literature review very few articles have been published on LITSEACUBEBIC ACID.
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0086473 (Litseacubebic acid)


  Mrv1652304292208462D          

 12 11  0  0  0  0            999 V2000
    2.8875    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7605    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    1.0164    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2375   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  2  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
 10 12  2  0  0  0  0
M  END
Download

3D MOL for NP0086473 (Litseacubebic acid)

     RDKit          3D

 26 25  0  0  0  0  0  0  0  0999 V2000
    2.5417   -1.5091   -0.6223 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5680   -0.1952    0.0367 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4405    0.4019    0.3263 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1267   -0.1555    0.0353 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9589    0.5064    0.3578 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3362    0.0189    0.1013 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2829   -0.9960   -1.0165 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2788    1.1689   -0.2231 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8027   -0.5807    1.2678 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8204    0.4667    0.3795 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9121   -0.0876    0.1111 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8663    1.6992    0.9979 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1046   -2.2988   -0.0031 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5941   -1.8054   -0.8735 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0058   -1.4554   -1.6054 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5027    1.3851    0.8198 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0540   -1.1113   -0.4445 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8249    1.4673    0.8407 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9269   -1.9485   -0.5776 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5904   -0.6253   -1.7797 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3035   -1.1399   -1.4567 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6742    1.9507   -0.7556 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6239    1.6470    0.7175 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0847    0.8773   -0.9020 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3319   -0.1718    2.0375 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4829    2.4911    0.4732 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  1  0
  6  8  1  0
  6  9  1  0
  2 10  1  0
 10 12  1  0
 10 11  2  0
  1 13  1  0
  1 14  1  0
  1 15  1  0
  3 16  1  0
  4 17  1  0
  5 18  1  0
  7 19  1  0
  7 20  1  0
  7 21  1  0
  8 22  1  0
  8 23  1  0
  8 24  1  0
  9 25  1  0
 12 26  1  0
M  END
Download

3D SDF for NP0086473 (Litseacubebic acid)


  Mrv1652304292208462D          

 12 11  0  0  0  0            999 V2000
    2.8875    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7605    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    1.0164    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2375   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  2  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
 10 12  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0086473

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C\C(=C/C=C/C(C)(C)O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C9H14O3/c1-7(8(10)11)5-4-6-9(2,3)12/h4-6,12H,1-3H3,(H,10,11)/b6-4+,7-5+

> <INCHI_KEY>
DIGXYNABEMPJKO-YDFGWWAZSA-N

> <FORMULA>
C9H14O3

> <MOLECULAR_WEIGHT>
170.208

> <EXACT_MASS>
170.094294311

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
26

> <JCHEM_AVERAGE_POLARIZABILITY>
18.581422895001943

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2E,4E)-6-hydroxy-2,6-dimethylhepta-2,4-dienoic acid

> <ALOGPS_LOGP>
1.50

> <JCHEM_LOGP>
1.2587289863333337

> <ALOGPS_LOGS>
-1.89

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
17.911528671585543

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.8644438677922786

> <JCHEM_PKA_STRONGEST_BASIC>
-1.5252975664947588

> <JCHEM_POLAR_SURFACE_AREA>
57.53

> <JCHEM_REFRACTIVITY>
48.472300000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.19e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2E,4E)-6-hydroxy-2,6-dimethylhepta-2,4-dienoic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0086473 (Litseacubebic acid)

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PDB for NP0086473 (Litseacubebic acid)
HEADER    PROTEIN                                 29-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   29-APR-22         0                                  
HETATM    1  C   UNK     0       5.390   4.001   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.620   2.667   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       3.286   3.437   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       5.954   1.897   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       3.850   1.334   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -0.770   1.334   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -0.770  -1.334   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       0.000  -2.667   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      -2.310  -1.334   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4    5                                             
CONECT    3    2                                                            
CONECT    4    2                                                            
CONECT    5    2    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   22    0
END

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3D PDB for NP0086473 (Litseacubebic acid)
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SMILES for NP0086473 (Litseacubebic acid)
C\C(=C/C=C/C(C)(C)O)C(O)=O
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INCHI for NP0086473 (Litseacubebic acid)
InChI=1S/C9H14O3/c1-7(8(10)11)5-4-6-9(2,3)12/h4-6,12H,1-3H3,(H,10,11)/b6-4+,7-5+
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View in JSmol
Synonyms
ValueSource
LITSEACUBEBateGenerator
Chemical FormulaC9H14O3
Average Mass170.2080 Da
Monoisotopic Mass170.09429 Da
IUPAC Name(2E,4E)-6-hydroxy-2,6-dimethylhepta-2,4-dienoic acid
Traditional Name(2E,4E)-6-hydroxy-2,6-dimethylhepta-2,4-dienoic acid
CAS Registry NumberNot Available
SMILES
C\C(=C/C=C/C(C)(C)O)C(O)=O
InChI Identifier
InChI=1S/C9H14O3/c1-7(8(10)11)5-4-6-9(2,3)12/h4-6,12H,1-3H3,(H,10,11)/b6-4+,7-5+
InChI KeyDIGXYNABEMPJKO-YDFGWWAZSA-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
Litsea cubebaPlant
Chemical Taxonomy
Description Belongs to the class of organic compounds known as medium-chain hydroxy acids and derivatives. These are hydroxy acids with a 6 to 12 carbon atoms long side chain.
KingdomOrganic compounds  
Super ClassOrganic acids and derivatives  
ClassHydroxy acids and derivatives  
Sub ClassMedium-chain hydroxy acids and derivatives  
Direct ParentMedium-chain hydroxy acids and derivatives  
Alternative Parents
Substituents
  • Medium-chain hydroxy acid
    • 

  • Medium-chain fatty acid
    • 

  • Branched fatty acid
    • 

  • Hydroxy fatty acid
    • 

  • Methyl-branched fatty acid
    • 

  • Fatty acyl
    • 

  • Fatty acid
    • 

  • Unsaturated fatty acid
    • 

  • Tertiary alcohol
    • 

  • Carboxylic acid derivative
    • 

  • Carboxylic acid
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Organic oxide
    • 

  • Alcohol
    • 

  • Carbonyl group
    • 

  • Hydrocarbon derivative
    • 

  • Organic oxygen compound
    • 

  • Organooxygen compound
    • 

  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic 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
logP1.5ALOGPS
logP1.26ChemAxon
logS-1.9ALOGPS
pKa (Strongest Acidic)4.86ChemAxon
pKa (Strongest Basic)-1.5ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area57.53 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity48.47 m³·mol⁻¹ChemAxon
Polarizability18.58 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDC00056755  
Chemspider ID31147516  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound76312534  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Yang Y, Jiang J, Qimei L, Yan X, Zhao J, Yuan H, Qin Z, Wang M: The fungicidal terpenoids and essential oil from Litsea cubeba in Tibet. Molecules. 2010 Oct 13;15(10):7075-82. doi: 10.3390/molecules15107075. [PubMed:20944522  ]