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Showing NP-Card for (2r,3r,4r,5s)-2-methylpiperidine-3,4,5-triol (NP0179663)

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Record Information
Version2.0
Created at2022-09-03 17:52:44 UTC
Updated at2022-09-03 17:52:44 UTC
NP-MRD IDNP0179663
Secondary Accession NumbersNone
Natural Product Identification
Common Name(2r,3r,4r,5s)-2-methylpiperidine-3,4,5-triol
Description1,6-Dideoxynojirimycin 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. (2r,3r,4r,5s)-2-methylpiperidine-3,4,5-triol is found in Angylocalyx pynaertii. (2r,3r,4r,5s)-2-methylpiperidine-3,4,5-triol was first documented in 2006 (PMID: 16815343). Based on a literature review a small amount of articles have been published on 1,6-dideoxynojirimycin (PMID: 19375073) (PMID: 18335959).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0179663 ((2r,3r,4r,5s)-2-methylpiperidine-3,4,5-triol)


  Mrv1652309032219522D          

 10 10  0  0  1  0            999 V2000
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  1  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
    1.4289   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  2  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
    0.0000    0.0000    0.0000 C   0  0  1  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
    0.0000    0.8250    0.0000 C   0  0  2  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
  2  1  1  1  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  6  0  0  0
  5  7  1  0  0  0  0
  7  8  1  1  0  0  0
  7  9  1  0  0  0  0
  2  9  1  0  0  0  0
  9 10  1  6  0  0  0
M  END
Download

3D MOL for NP0179663 ((2r,3r,4r,5s)-2-methylpiperidine-3,4,5-triol)

     RDKit          3D

 23 23  0  0  0  0  0  0  0  0999 V2000
    2.4227    0.0050    0.8185 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2200   -0.0072   -0.1353 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.8218   -1.3675   -0.2864 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4662   -1.4420   -0.9694 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4627   -0.8574    0.0423 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.7460   -1.2061   -0.2823 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2065    0.6250    0.0533 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.0621    1.1874    1.0154 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2017    0.9112    0.4145 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.5026    2.2139   -0.0460 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9550    0.9448    0.6846 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9878   -0.0130    1.8540 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0461   -0.8949    0.6467 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6121    0.3368   -1.1324 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5113   -1.8590   -0.8845 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7094   -2.4774   -1.1984 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4787   -0.7657   -1.8664 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1959   -1.2351    1.0605 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3255   -0.4387   -0.4541 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4935    1.0530   -0.9338 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8955    2.1485    1.1282 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2774    0.9728    1.5205 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4834    2.1656   -1.0497 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
  5  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
  9  2  1  0
  1 11  1  0
  1 12  1  0
  1 13  1  0
  2 14  1  6
  3 15  1  0
  4 16  1  0
  4 17  1  0
  5 18  1  1
  6 19  1  0
  7 20  1  6
  8 21  1  0
  9 22  1  1
 10 23  1  0
M  END
Download

3D SDF for NP0179663 ((2r,3r,4r,5s)-2-methylpiperidine-3,4,5-triol)


  Mrv1652309032219522D          

 10 10  0  0  1  0            999 V2000
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  1  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
    1.4289   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  2  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
    0.0000    0.0000    0.0000 C   0  0  1  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
    0.0000    0.8250    0.0000 C   0  0  2  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
  2  1  1  1  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  6  0  0  0
  5  7  1  0  0  0  0
  7  8  1  1  0  0  0
  7  9  1  0  0  0  0
  2  9  1  0  0  0  0
  9 10  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0179663

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@H]1NC[C@H](O)[C@@H](O)[C@@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C6H13NO3/c1-3-5(9)6(10)4(8)2-7-3/h3-10H,2H2,1H3/t3-,4+,5-,6-/m1/s1

> <INCHI_KEY>
VYOCYWDJTQRZLC-JGWLITMVSA-N

> <FORMULA>
C6H13NO3

> <MOLECULAR_WEIGHT>
147.174

> <EXACT_MASS>
147.089543283

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
23

> <JCHEM_AVERAGE_POLARIZABILITY>
14.838452748065574

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3R,4R,5S)-2-methylpiperidine-3,4,5-triol

> <JCHEM_LOGP>
-1.8388332163333334

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
14.126368575250961

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.933748576590272

> <JCHEM_PKA_STRONGEST_BASIC>
8.62129395686584

> <JCHEM_POLAR_SURFACE_AREA>
72.72

> <JCHEM_REFRACTIVITY>
35.030699999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3R,4R,5S)-2-methylpiperidine-3,4,5-triol

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0179663 ((2r,3r,4r,5s)-2-methylpiperidine-3,4,5-triol)

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PDB for NP0179663 ((2r,3r,4r,5s)-2-methylpiperidine-3,4,5-triol)
HEADER    PROTEIN                                 03-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-SEP-22         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   2.310   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0       2.667   1.540   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -1.334  -0.770   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -1.334   2.310   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    9                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7    2   10                                                  
CONECT   10    9                                                            
MASTER        0    0    0    0    0    0    0    0   10    0   20    0
END

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3D PDB for NP0179663 ((2r,3r,4r,5s)-2-methylpiperidine-3,4,5-triol)
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SMILES for NP0179663 ((2r,3r,4r,5s)-2-methylpiperidine-3,4,5-triol)
C[C@H]1NC[C@H](O)[C@@H](O)[C@@H]1O
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INCHI for NP0179663 ((2r,3r,4r,5s)-2-methylpiperidine-3,4,5-triol)
InChI=1S/C6H13NO3/c1-3-5(9)6(10)4(8)2-7-3/h3-10H,2H2,1H3/t3-,4+,5-,6-/m1/s1
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View in JSmol
SynonymsNot Available
Chemical FormulaC6H13NO3
Average Mass147.1740 Da
Monoisotopic Mass147.08954 Da
IUPAC Name(2R,3R,4R,5S)-2-methylpiperidine-3,4,5-triol
Traditional Name(2R,3R,4R,5S)-2-methylpiperidine-3,4,5-triol
CAS Registry NumberNot Available
SMILES
C[C@H]1NC[C@H](O)[C@@H](O)[C@@H]1O
InChI Identifier
InChI=1S/C6H13NO3/c1-3-5(9)6(10)4(8)2-7-3/h3-10H,2H2,1H3/t3-,4+,5-,6-/m1/s1
InChI KeyVYOCYWDJTQRZLC-JGWLITMVSA-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
Angylocalyx pynaertiiLOTUS 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
    • 

  • Secondary alcohol
    • 

  • 1,2-aminoalcohol
    • 

  • Azacycle
    • 

  • Secondary amine
    • 

  • Polyol
    • 

  • Secondary aliphatic amine
    • 

  • Organic nitrogen compound
    • 

  • Organic oxygen compound
    • 

  • Hydrocarbon derivative
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • Amine
    • 

  • Alcohol
    • 

  • 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-1.8ChemAxon
pKa (Strongest Acidic)12.93ChemAxon
pKa (Strongest Basic)8.62ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area72.72 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity35.03 m³·mol⁻¹ChemAxon
Polarizability14.84 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID8527287  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound10351835  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Simak O, Stanek J, Moravcova J: A stereocontrolled synthesis of 3-acetamido-1,3,5-trideoxy- and 1,3,5,6-tetradeoxy-1,5-imino-D-glucitol. Carbohydr Res. 2009 May 26;344(8):966-71. doi: 10.1016/j.carres.2009.03.016. Epub  2009 Mar 21. [PubMed:19375073  ] 
  2. Rengasamy R, Curtis-Long MJ, Seo WD, Jeong SH, Jeong IY, Park KH: New building block for polyhydroxylated piperidine: total synthesis of 1,6-dideoxynojirimycin. J Org Chem. 2008 Apr 4;73(7):2898-901. doi: 10.1021/jo702480y. Epub 2008 Mar 12. [PubMed:18335959  ] 
  3. An JN, Meng XB, Yao Y, Li ZJ: A facile synthesis of 1,6-dideoxynojirimycin from L-sorbose. Carbohydr Res. 2006 Sep 25;341(13):2200-3. doi: 10.1016/j.carres.2006.06.002.  Epub 2006 Jul 3. [PubMed:16815343  ] 
  4. LOTUS database [Link]