Np mrd loader

Showing NP-Card for 2-methylpiperidine-3,4-diol (NP0152943)

Jump To Section:
IdentificationSpectraBioTaxonomyChemoTaxonomyPhysical propertiesLinksReferencesXML
Record Information
Version2.0
Created at2022-09-02 09:31:32 UTC
Updated at2022-09-02 09:31:32 UTC
NP-MRD IDNP0152943
Secondary Accession NumbersNone
Natural Product Identification
Common Name2-methylpiperidine-3,4-diol
Description6-Deoxyfagomine 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. 2-methylpiperidine-3,4-diol is found in Lycium chinense. 6-Deoxyfagomine is a very strong basic compound (based on its pKa).
Structure
Thumb
MOL3D MOLSDFPDBSMILESInChI

MOL for NP0152943 (2-methylpiperidine-3,4-diol)


  Mrv0541 05061309062D          

  9  9  0  0  0  0            999 V2000
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    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
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  1  0  0  0  0
  4  1  1  0  0  0  0
  5  2  1  0  0  0  0
  6  4  1  0  0  0  0
  6  5  1  0  0  0  0
  7  3  1  0  0  0  0
  7  4  1  0  0  0  0
  8  5  1  0  0  0  0
  9  6  1  0  0  0  0
M  END
Download

3D MOL for NP0152943 (2-methylpiperidine-3,4-diol)

     RDKit          3D

 22 22  0  0  0  0  0  0  0  0999 V2000
    2.3153   -0.9410   -0.2300 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0524   -0.1596   -0.2872 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.9399    0.8648    0.7221 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1104    1.7643    0.3086 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4360    1.0060    0.4746 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3597   -0.1550   -0.5039 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.5303   -0.8781   -0.4201 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1922   -1.0391   -0.1020 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.3050   -1.2322    1.2839 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1171   -0.3437   -0.7164 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1801   -1.8653   -0.8412 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6627   -1.1651    0.7886 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9607    0.2825   -1.3068 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8142    1.3097    0.9891 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0636    1.9977   -0.7906 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1165    2.7208    0.8438 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4384    0.6139    1.4914 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2906    1.6604    0.2669 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1629    0.1850   -1.5408 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0899   -0.6039   -1.2074 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1382   -1.9643   -0.6670 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8088   -2.0577    1.4446 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  1  0
  8  2  1  0
  1 10  1  0
  1 11  1  0
  1 12  1  0
  2 13  1  6
  3 14  1  0
  4 15  1  0
  4 16  1  0
  5 17  1  0
  5 18  1  0
  6 19  1  6
  7 20  1  0
  8 21  1  6
  9 22  1  0
M  END
Download

3D SDF for NP0152943 (2-methylpiperidine-3,4-diol)


  Mrv0541 05061309062D          

  9  9  0  0  0  0            999 V2000
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    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
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  1  0  0  0  0
  4  1  1  0  0  0  0
  5  2  1  0  0  0  0
  6  4  1  0  0  0  0
  6  5  1  0  0  0  0
  7  3  1  0  0  0  0
  7  4  1  0  0  0  0
  8  5  1  0  0  0  0
  9  6  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0152943

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC1NCCC(O)C1O

> <INCHI_IDENTIFIER>
InChI=1S/C6H13NO2/c1-4-6(9)5(8)2-3-7-4/h4-9H,2-3H2,1H3

> <INCHI_KEY>
RMJCALHKIHCSMY-UHFFFAOYSA-N

> <FORMULA>
C6H13NO2

> <MOLECULAR_WEIGHT>
131.1729

> <EXACT_MASS>
131.094628665

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
14.085088841210318

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-methylpiperidine-3,4-diol

> <ALOGPS_LOGP>
-0.93

> <JCHEM_LOGP>
-1.1485385353333335

> <ALOGPS_LOGS>
0.62

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
15.078728287233382

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.508061802678977

> <JCHEM_PKA_STRONGEST_BASIC>
9.206712594276363

> <JCHEM_POLAR_SURFACE_AREA>
52.489999999999995

> <JCHEM_REFRACTIVITY>
33.9336

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.42e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-methylpiperidine-3,4-diol

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0152943 (2-methylpiperidine-3,4-diol)

Download
PDB for NP0152943 (2-methylpiperidine-3,4-diol)
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       1.334   3.850   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       2.667   1.540   0.000  0.00  0.00           N+0
HETATM    8  O   UNK     0      -1.334  -0.770   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      -1.334   2.310   0.000  0.00  0.00           O+0
CONECT    1    4                                                            
CONECT    2    3    5                                                       
CONECT    3    2    7                                                       
CONECT    4    1    6    7                                                  
CONECT    5    2    6    8                                                  
CONECT    6    4    5    9                                                  
CONECT    7    3    4                                                       
CONECT    8    5                                                            
CONECT    9    6                                                            
MASTER        0    0    0    0    0    0    0    0    9    0   18    0
END

Download
3D PDB for NP0152943 (2-methylpiperidine-3,4-diol)
Download
SMILES for NP0152943 (2-methylpiperidine-3,4-diol)
CC1NCCC(O)C1O
Download
INCHI for NP0152943 (2-methylpiperidine-3,4-diol)
InChI=1S/C6H13NO2/c1-4-6(9)5(8)2-3-7-4/h4-9H,2-3H2,1H3
Download
View in JSmol
Synonyms
ValueSource
(-)-6-Deoxy-fagomineHMDB
6-Deoxy-fagomineHMDB
Chemical FormulaC6H13NO2
Average Mass131.1729 Da
Monoisotopic Mass131.09463 Da
IUPAC Name2-methylpiperidine-3,4-diol
Traditional Name2-methylpiperidine-3,4-diol
CAS Registry NumberNot Available
SMILES
CC1NCCC(O)C1O
InChI Identifier
InChI=1S/C6H13NO2/c1-4-6(9)5(8)2-3-7-4/h4-9H,2-3H2,1H3
InChI KeyRMJCALHKIHCSMY-UHFFFAOYSA-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
Lycium chinenseLOTUS 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
  • Piperidine
    • 

  • 1,2-aminoalcohol
    • 

  • 1,2-diol
    • 

  • Secondary alcohol
    • 

  • Secondary aliphatic amine
    • 

  • Azacycle
    • 

  • Secondary amine
    • 

  • Organic nitrogen compound
    • 

  • Hydrocarbon derivative
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • Organopnictogen compound
    • 

  • Amine
    • 

  • Alcohol
    • 

  • Organic oxygen compound
    • 

  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic 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
logP-0.93ALOGPS
logP-1.1ChemAxon
logS0.62ALOGPS
pKa (Strongest Acidic)13.51ChemAxon
pKa (Strongest Basic)9.21ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area52.49 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity33.93 m³·mol⁻¹ChemAxon
Polarizability14.09 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0036382  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB015260  
KNApSAcK IDC00036613  
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound57449463  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. LOTUS database [Link]