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Showing NP-Card for Pinidine (NP0051143)

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Record Information
Version2.0
Created at2022-04-27 22:33:29 UTC
Updated at2022-04-27 22:33:30 UTC
NP-MRD IDNP0051143
Secondary Accession NumbersNone
Natural Product Identification
Common NamePinidine
DescriptionPinidine belongs to the class of organic compounds known as piperidines. Piperidines are compounds containing a piperidine ring, which is a saturated aliphatic six-member ring with one nitrogen atom and five carbon atoms. Pinidine is found in Picea pungens, Pinus jeffreyi, Pinus koraiensis , Pinus ponderosa, Pinus sabiniana and Pinus torreyana . Pinidine was first documented in 2003 (PMID: 14677980). Pinidine is a very strong basic compound (based on its pKa) (PMID: 24105602).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0051143 (Pinidine)


  Mrv1652309272006262D          

 10 10  0  0  0  0            999 V2000
   -1.7187    1.5392    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4332    1.1267    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4332    0.3016    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.7187   -0.1107    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0042    0.3016    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.0042    1.1267    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2898   -0.1108    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4246    0.3015    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1391   -0.1109    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1476   -0.1108    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  6  1  0  0  0  0
  2  3  1  0  0  0  0
  5  6  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  7  1  6  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  3 10  1  6  0  0  0
M  END
Download

3D MOL for NP0051143 (Pinidine)

     RDKit          3D

 27 27  0  0  0  0  0  0  0  0999 V2000
    4.2185    0.3617    0.1140 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8586    0.3492   -0.4762 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7838   -0.0126    0.1979 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4266   -0.0204   -0.4062 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0084   -1.4233   -0.6251 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4423   -1.6772   -0.7133 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3400   -0.5893   -0.2735 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7417    0.7832   -0.3305 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.7015    1.8031    0.1950 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5030    0.7405    0.4314 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.3303   -0.5044    0.8118 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0093    0.2804   -0.6363 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3733    1.2839    0.7132 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7052    0.6485   -1.5169 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8961   -0.3154    1.2308 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4697    0.5511   -1.3793 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4978   -1.7779   -1.5806 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5035   -2.0546    0.1696 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7392   -2.0000   -1.7543 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6726   -2.5872   -0.0839 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2677   -0.5672   -0.9048 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7165   -0.7325    0.7786 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4803    1.0613   -1.3809 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1336    1.5248    1.1609 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1636    2.7709    0.3185 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5054    1.9246   -0.5752 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6739    0.1787    1.3126 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  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  8 10  1  0
 10  4  1  0
  1 11  1  0
  1 12  1  0
  1 13  1  0
  2 14  1  0
  3 15  1  0
  4 16  1  6
  5 17  1  0
  5 18  1  0
  6 19  1  0
  6 20  1  0
  7 21  1  0
  7 22  1  0
  8 23  1  6
  9 24  1  0
  9 25  1  0
  9 26  1  0
 10 27  1  0
M  END
Download

3D SDF for NP0051143 (Pinidine)


  Mrv1652309272006262D          

 10 10  0  0  0  0            999 V2000
   -1.7187    1.5392    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4332    1.1267    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4332    0.3016    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.7187   -0.1107    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0042    0.3016    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.0042    1.1267    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2898   -0.1108    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4246    0.3015    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1391   -0.1109    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1476   -0.1108    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  6  1  0  0  0  0
  2  3  1  0  0  0  0
  5  6  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  7  1  6  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  3 10  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0051143

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C\C=C\[C@H]1CCC[C@@H](C)N1

> <INCHI_IDENTIFIER>
InChI=1S/C9H17N/c1-3-5-9-7-4-6-8(2)10-9/h3,5,8-10H,4,6-7H2,1-2H3/b5-3+/t8-,9+/m1/s1

> <INCHI_KEY>
CXQRNYIKPJXYLU-ZHBVTVBMSA-N

> <FORMULA>
C9H17N

> <MOLECULAR_WEIGHT>
139.242

> <EXACT_MASS>
139.136099551

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
27

> <JCHEM_AVERAGE_POLARIZABILITY>
17.83331971048075

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,6R)-2-methyl-6-[(1E)-prop-1-en-1-yl]piperidine

> <ALOGPS_LOGP>
2.47

> <JCHEM_LOGP>
2.2517145726666663

> <ALOGPS_LOGS>
-2.11

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_BASIC>
9.854128656469648

> <JCHEM_POLAR_SURFACE_AREA>
12.03

> <JCHEM_REFRACTIVITY>
45.7606

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.08e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
pinidine

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for NP0051143 (Pinidine)

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PDB for NP0051143 (Pinidine)
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      -3.208   2.873   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -4.542   2.103   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -4.542   0.563   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0      -3.208  -0.207   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0      -1.875   0.563   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -1.875   2.103   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -0.541  -0.207   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.793   0.563   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.126  -0.207   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -5.876  -0.207   0.000  0.00  0.00           C+0
CONECT    1    2    6                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4   10                                                  
CONECT    4    3    5                                                       
CONECT    5    6    4    7                                                  
CONECT    6    1    5                                                       
CONECT    7    5    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8                                                            
CONECT   10    3                                                            
MASTER        0    0    0    0    0    0    0    0   10    0   20    0
END

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3D PDB for NP0051143 (Pinidine)
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SMILES for NP0051143 (Pinidine)
C\C=C\[C@H]1CCC[C@@H](C)N1
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INCHI for NP0051143 (Pinidine)
InChI=1S/C9H17N/c1-3-5-9-7-4-6-8(2)10-9/h3,5,8-10H,4,6-7H2,1-2H3/b5-3+/t8-,9+/m1/s1
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View in JSmol
Synonyms
ValueSource
(-)-PinidineChEBI
[2R-[2alpha,6alpha(E)]]-2-Methyl-6-(1-propenyl)-piperidinePhytoBank
[2R-[2α,6α(E)]]-2-Methyl-6-(1-propenyl)-piperidinePhytoBank
(2R,6R)-2-Methyl-6-(1E)-1-propenylpiperidinePhytoBank
(2R,6R)-2-Methyl-6-(1E)-1-propen-1-ylpiperidinePhytoBank
cis-(-)-6-Propenyl-2-pipecolinePhytoBank
Chemical FormulaC9H17N
Average Mass139.2420 Da
Monoisotopic Mass139.13610 Da
IUPAC Name(2R,6R)-2-methyl-6-[(1E)-prop-1-en-1-yl]piperidine
Traditional Namepinidine
CAS Registry NumberNot Available
SMILES
C\C=C\[C@H]1CCC[C@@H](C)N1
InChI Identifier
InChI=1S/C9H17N/c1-3-5-9-7-4-6-8(2)10-9/h3,5,8-10H,4,6-7H2,1-2H3/b5-3+/t8-,9+/m1/s1
InChI KeyCXQRNYIKPJXYLU-ZHBVTVBMSA-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
Picea pungensLOTUS Database
Pinus jeffreyiPlant
Pinus koraiensisPlant
Pinus ponderosaPlant
Pinus sabinianaPlant
Pinus torreyanaPlant
Chemical Taxonomy
Description Belongs to the class of organic compounds known as piperidines. Piperidines are compounds containing a piperidine ring, which is a saturated aliphatic six-member ring with one nitrogen atom and five carbon atoms.
KingdomOrganic compounds  
Super ClassOrganoheterocyclic compounds  
ClassPiperidines  
Sub ClassNot Available
Direct ParentPiperidines  
Alternative Parents
Substituents
  • Piperidine
    • 

  • Azacycle
    • 

  • Secondary amine
    • 

  • Secondary aliphatic amine
    • 

  • Organic nitrogen compound
    • 

  • Organopnictogen compound
    • 

  • Hydrocarbon derivative
    • 

  • Organonitrogen compound
    • 

  • Amine
    • 

  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic 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
logP2.47ALOGPS
logP2.25ChemAxon
logS-2.1ALOGPS
pKa (Strongest Basic)9.85ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area12.03 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity45.76 m³·mol⁻¹ChemAxon
Polarizability17.83 ųChemAxon
Number of Rings1ChemAxon
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 IDC00002064  
Chemspider ID4445006  
KEGG Compound IDC10165  
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound5281689  
PDB IDNot Available
ChEBI ID8217  
Good Scents IDNot Available
References
General References
  1. Virjamo V, Julkunen-Tiitto R, Henttonen H, Hiltunen E, Karjalainen R, Korhonen J, Huitu O: Differences in vole preference, secondary chemistry and nutrient levels between naturally regenerated and planted Norway spruce seedlings. J Chem Ecol. 2013 Oct;39(10):1322-34. doi: 10.1007/s10886-013-0352-6. Epub 2013  Oct 9. [PubMed:24105602  ] 
  2. Hong S, Kawaoka AM, Marks TJ: Intramolecular hydroamination/cyclization of conjugated aminodienes catalyzed by organolanthanide complexes. Scope, diastereo- and enantioselectivity, and reaction mechanism. J Am Chem Soc. 2003 Dec 24;125(51):15878-92. doi: 10.1021/ja036266y. [PubMed:14677980  ]