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Showing NP-Card for (-)-pinidinone (NP0200468)

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Record Information
Version2.0
Created at2022-09-04 19:19:25 UTC
Updated at2022-09-04 19:19:26 UTC
NP-MRD IDNP0200468
Secondary Accession NumbersNone
Natural Product Identification
Common Name(-)-pinidinone
Description(-)-Pinidinone belongs to the class of organic compounds known as piperidines. (-)-pinidinone is found in Picea pungens and Pinus ponderosa. (-)-pinidinone was first documented in 2011 (PMID: 21410219). Piperidines are compounds containing a piperidine ring, which is a saturated aliphatic six-member ring with one nitrogen atom and five carbon atoms (-)-pinidinone is a very strong basic compound (based on its pKa).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0200468 ((-)-pinidinone)


  Mrv1652309272006412D          

 11 11  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
    0.4247    1.1265    0.0000 O   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  1  0  0  0  0
  8  9  1  0  0  0  0
  3 10  1  6  0  0  0
  8 11  2  0  0  0  0
M  END
Download

3D MOL for NP0200468 ((-)-pinidinone)

     RDKit          3D

 28 28  0  0  0  0  0  0  0  0999 V2000
    2.7486   -1.2018    0.0914 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6194    0.0344   -0.7131 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4645    0.2340   -1.5699 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5356    1.0191   -0.5307 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5719    0.6205    0.5647 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.5057    1.6598    0.7026 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4994    1.6294   -0.4310 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6964    0.1969   -0.9414 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3881   -0.6865    0.2522 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.9694   -2.0348    0.0235 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0532   -0.7142    0.3889 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.7827   -1.6030    0.0449 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6107   -0.8910    1.1631 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0669   -2.0048   -0.2140 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0184    1.2918   -1.4653 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0199    1.9739   -0.1726 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1510    0.6191    1.5120 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    2.6570    0.6512 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0016    1.6196    1.6911 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4888    1.9346   -0.0231 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2502    2.2876   -1.2637 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9630   -0.0341   -1.7414 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7328    0.0508   -1.3139 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8551   -0.2210    1.1422 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6115   -2.7943    0.7518 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8510   -2.3577   -1.0288 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0843   -1.9502    0.1787 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2545   -1.3353    1.2091 H   0  0  0  0  0  0  0  0  0  0  0  0
 10  9  1  0
  9  8  1  0
  8  7  1  0
  7  6  1  0
  6  5  1  0
  5  4  1  0
  4  2  1  0
  2  1  1  0
  2  3  2  0
  5 11  1  0
 11  9  1  0
 10 25  1  0
 10 26  1  0
 10 27  1  0
  9 24  1  1
  8 22  1  0
  8 23  1  0
  7 20  1  0
  7 21  1  0
  6 18  1  0
  6 19  1  0
  5 17  1  1
  4 15  1  0
  4 16  1  0
  1 12  1  0
  1 13  1  0
  1 14  1  0
 11 28  1  0
M  END
Download

3D SDF for NP0200468 ((-)-pinidinone)


  Mrv1652309272006412D          

 11 11  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
    0.4247    1.1265    0.0000 O   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  1  0  0  0  0
  8  9  1  0  0  0  0
  3 10  1  6  0  0  0
  8 11  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0200468

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C9H17NO/c1-7-4-3-5-9(10-7)6-8(2)11/h7,9-10H,3-6H2,1-2H3/t7-,9-/m1/s1

> <INCHI_KEY>
PLVQSRXCDPEDHN-VXNVDRBHSA-N

> <FORMULA>
C9H17NO

> <MOLECULAR_WEIGHT>
155.241

> <EXACT_MASS>
155.131014171

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
28

> <JCHEM_AVERAGE_POLARIZABILITY>
18.375729154056163

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1-[(2R,6R)-6-methylpiperidin-2-yl]propan-2-one

> <ALOGPS_LOGP>
1.21

> <JCHEM_LOGP>
1.178451322

> <ALOGPS_LOGS>
-1.20

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_ACIDIC>
18.501633712319073

> <JCHEM_PKA_STRONGEST_BASIC>
9.95131204876789

> <JCHEM_POLAR_SURFACE_AREA>
29.1

> <JCHEM_REFRACTIVITY>
45.259499999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
9.71e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1-[(2R,6R)-6-methylpiperidin-2-yl]propan-2-one

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for NP0200468 ((-)-pinidinone)

Download
PDB for NP0200468 ((-)-pinidinone)
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
HETATM   11  O   UNK     0       0.793   2.103   0.000  0.00  0.00           O+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   11                                                  
CONECT    9    8                                                            
CONECT   10    3                                                            
CONECT   11    8                                                            
MASTER        0    0    0    0    0    0    0    0   11    0   22    0
END

Download
3D PDB for NP0200468 ((-)-pinidinone)
Download
SMILES for NP0200468 ((-)-pinidinone)
C[C@@H]1CCC[C@H](CC(C)=O)N1
Download
INCHI for NP0200468 ((-)-pinidinone)
InChI=1S/C9H17NO/c1-7-4-3-5-9(10-7)6-8(2)11/h7,9-10H,3-6H2,1-2H3/t7-,9-/m1/s1
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View in JSmol
Synonyms
ValueSource
(2R-cis)-1-(6-Methyl-2-piperidinyl)-2-propanonePhytoBank
1-[(2R,6R)-6-Methyl-2-piperidinyl]-2-propanonePhytoBank
(-)-PinidinonePhytoBank
Chemical FormulaC9H17NO
Average Mass155.2410 Da
Monoisotopic Mass155.13101 Da
IUPAC Name1-[(2R,6R)-6-methylpiperidin-2-yl]propan-2-one
Traditional Name1-[(2R,6R)-6-methylpiperidin-2-yl]propan-2-one
CAS Registry NumberNot Available
SMILES
C[C@@H]1CCC[C@H](CC(C)=O)N1
InChI Identifier
InChI=1S/C9H17NO/c1-7-4-3-5-9(10-7)6-8(2)11/h7,9-10H,3-6H2,1-2H3/t7-,9-/m1/s1
InChI KeyPLVQSRXCDPEDHN-VXNVDRBHSA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Picea pungensLOTUS Database
Pinus ponderosaLOTUS Database
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
  • Beta-aminoketone
    • 

  • Piperidine
    • 

  • Ketone
    • 

  • Secondary aliphatic amine
    • 

  • Secondary amine
    • 

  • Azacycle
    • 

  • Amine
    • 

  • Organopnictogen compound
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • Organic oxygen compound
    • 

  • Carbonyl group
    • 

  • Organic nitrogen compound
    • 

  • Hydrocarbon derivative
    • 

  • Organic oxide
    • 

  • 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
logP1.21ALOGPS
logP1.18ChemAxon
logS-1.2ALOGPS
pKa (Strongest Acidic)18.5ChemAxon
pKa (Strongest Basic)9.95ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area29.1 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity45.26 m³·mol⁻¹ChemAxon
Polarizability18.38 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 IDNot Available
Chemspider ID9334543  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound11159443  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Kavala M, Mathia F, Kozisek J, Szolcsanyi P: Efficient total synthesis of (+)-dihydropinidine, (-)-epidihydropinidine, and (-)-pinidinone. J Nat Prod. 2011 Apr 25;74(4):803-8. doi: 10.1021/np100852p. Epub 2011 Mar 16. [PubMed:21410219  ] 
  2. LOTUS database [Link]