NP-MRD: Showing NP-Card for 6-[(3s,5r)-5-(hydroxymethyl)-1-methylpiperidin-3-yl]pyridin-2-ol (NP0290677)

Jump To Section:

Identification Spectra BioTaxonomy ChemoTaxonomy Physical properties Links References XML

Record Information

Version

2.0

Created at

2022-09-09 21:28:11 UTC

Updated at

2022-09-09 21:28:11 UTC

NP-MRD ID

NP0290677

Secondary Accession Numbers

None

Natural Product Identification

Common Name

6-[(3s,5r)-5-(hydroxymethyl)-1-methylpiperidin-3-yl]pyridin-2-ol

Description

Kuraramine belongs to the class of organic compounds known as pyridinones. Pyridinones are compounds containing a pyridine ring, which bears a ketone. 6-[(3s,5r)-5-(hydroxymethyl)-1-methylpiperidin-3-yl]pyridin-2-ol is found in Sophora chrysophylla. 6-[(3s,5r)-5-(hydroxymethyl)-1-methylpiperidin-3-yl]pyridin-2-ol was first documented in 2005 (PMID: 15651792). Based on a literature review very few articles have been published on Kuraramine.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 34 35  0  0  0  0  0  0  0  0999 V2000
   -2.0392   -2.5158   -1.1588 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4720   -1.2144   -1.0583 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1045   -1.1238   -0.8008 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3349   -0.3905    0.4043 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.7425    0.0604    0.2035 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0817    0.9490   -0.8070 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3756    1.3795   -1.0113 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3776    0.9180   -0.1890 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0323    0.0357    0.8121 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0725   -0.4152    1.6311 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7605   -0.3589    0.9777 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5719    0.7510    0.8043 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9802    0.2007    0.8145 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.9618    1.1442    1.4443 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0907    2.3353    0.7666 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3226   -0.1921   -0.5854 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9352   -2.4344   -1.8420 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3617   -2.8530   -0.1594 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3024   -3.1847   -1.6364 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4102   -0.6731   -1.6997 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3295   -2.1652   -0.7465 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3549   -1.0929    1.2752 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2881    1.3059   -1.4477 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6404    2.0737   -1.8009 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4233    1.2397   -0.3218 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9630   -0.4850    2.6230 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2444    1.1256    1.7884 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5307    1.5633    0.0271 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9548   -0.7166    1.4519 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9463    0.6411    1.4580 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6589    1.2824    2.5017 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0241    2.6784    0.9332 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3746   -0.6033   -0.5576 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3109    0.7353   -1.2062 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2 16  1  0
 16 13  1  0
 13 14  1  0
 14 15  1  0
 13 12  1  0
 12  4  1  0
  4  3  1  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  1  0
  9 11  2  0
  3  2  1  0
 11  5  1  0
  1 17  1  0
  1 18  1  0
  1 19  1  0
 16 33  1  0
 16 34  1  0
 13 29  1  1
 14 30  1  0
 14 31  1  0
 15 32  1  0
 12 27  1  0
 12 28  1  0
  4 22  1  1
  3 20  1  0
  3 21  1  0
  6 23  1  0
  7 24  1  0
  8 25  1  0
 10 26  1  0
M  END


  Mrv1652309092223282D          

 16 17  0  0  1  0            999 V2000
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -2.4750    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.1434   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -4.9500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -3.7125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -2.4750    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7145   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.6500    0.0000 C   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
  3  4  1  0  0  0  0
  4  5  1  1  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
  9 10  1  0  0  0  0
  9 11  2  0  0  0  0
  5 11  1  0  0  0  0
  4 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  1  0  0  0
 14 15  1  0  0  0  0
 13 16  1  0  0  0  0
  2 16  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0290677

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CN1C[C@H](CO)C[C@@H](C1)C1=CC=CC(O)=N1

> <INCHI_IDENTIFIER>
InChI=1S/C12H18N2O2/c1-14-6-9(8-15)5-10(7-14)11-3-2-4-12(16)13-11/h2-4,9-10,15H,5-8H2,1H3,(H,13,16)/t9-,10+/m1/s1

> <INCHI_KEY>
CUHBAHMWNDOHGZ-ZJUUUORDSA-N

> <FORMULA>
C12H18N2O2

> <MOLECULAR_WEIGHT>
222.288

> <EXACT_MASS>
222.136827828

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
34

> <JCHEM_AVERAGE_POLARIZABILITY>
24.809160240612762

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
6-[(3S,5R)-5-(hydroxymethyl)-1-methylpiperidin-3-yl]pyridin-2-ol

> <JCHEM_LOGP>
0.7902199879999999

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
15.430451222095062

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.815504821458827

> <JCHEM_PKA_STRONGEST_BASIC>
8.28282860070768

> <JCHEM_POLAR_SURFACE_AREA>
56.59

> <JCHEM_REFRACTIVITY>
62.660799999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
6-[(3S,5R)-5-(hydroxymethyl)-1-methylpiperidin-3-yl]pyridin-2-ol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 09-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   09-SEP-22         0                                  
HETATM    1  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0       1.334  -2.310   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.001  -5.390   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       6.668  -5.390   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       6.668  -6.930   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       5.335  -7.700   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       5.335  -9.240   0.000  0.00  0.00           O+0
HETATM   11  N   UNK     0       4.001  -6.930   0.000  0.00  0.00           N+0
HETATM   12  C   UNK     0       1.334  -5.390   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       0.000  -4.620   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -1.334  -5.390   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      -1.334  -6.930   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       0.000  -3.080   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   16                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   12                                                  
CONECT    5    4    6   11                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9    5                                                       
CONECT   12    4   13                                                       
CONECT   13   12   14   16                                                  
CONECT   14   13   15                                                       
CONECT   15   14                                                            
CONECT   16   13    2                                                       
MASTER        0    0    0    0    0    0    0    0   16    0   34    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₂H₁₈N₂O₂

Average Mass

222.2880 Da

Monoisotopic Mass

222.13683 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

CN1C[C@H](CO)C[C@@H](C1)C1=CC=CC(O)=N1

InChI Identifier

InChI=1S/C12H18N2O2/c1-14-6-9(8-15)5-10(7-14)11-3-2-4-12(16)13-11/h2-4,9-10,15H,5-8H2,1H3,(H,13,16)/t9-,10+/m1/s1

InChI Key

CUHBAHMWNDOHGZ-ZJUUUORDSA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Sophora chrysophylla	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyridinones. Pyridinones are compounds containing a pyridine ring, which bears a ketone.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Pyridines and derivatives

Sub Class

Hydropyridines

Direct Parent

Pyridinones

Alternative Parents

Substituents

Dihydropyridine
Pyridinone
Aralkylamine
Piperidine
1,3-aminoalcohol
Heteroaromatic compound
Tertiary aliphatic amine
Tertiary amine
Lactam
Azacycle
Hydrocarbon derivative
Organic oxide
Primary alcohol
Organic oxygen compound
Organooxygen compound
Organonitrogen compound
Organic nitrogen compound
Amine
Alcohol
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00007783

Chemspider ID

9622247

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

11447394

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Honda T, Takahashi R, Namiki H: Syntheses of (+)-cytisine, (-)-kuraramine, (-)-isokuraramine, and (-)-jussiaeiine A. J Org Chem. 2005 Jan 21;70(2):499-504. doi: 10.1021/jo048365f. [PubMed:15651792 ]
LOTUS database [Link]

Showing NP-Card for 6-[(3s,5r)-5-(hydroxymethyl)-1-methylpiperidin-3-yl]pyridin-2-ol (NP0290677)

MOL for NP0290677 (6-[(3s,5r)-5-(hydroxymethyl)-1-methylpiperidin-3-yl]pyridin-2-ol)

3D MOL for NP0290677 (6-[(3s,5r)-5-(hydroxymethyl)-1-methylpiperidin-3-yl]pyridin-2-ol)

3D SDF for NP0290677 (6-[(3s,5r)-5-(hydroxymethyl)-1-methylpiperidin-3-yl]pyridin-2-ol)

3D-SDF for NP0290677 (6-[(3s,5r)-5-(hydroxymethyl)-1-methylpiperidin-3-yl]pyridin-2-ol)

PDB for NP0290677 (6-[(3s,5r)-5-(hydroxymethyl)-1-methylpiperidin-3-yl]pyridin-2-ol)

3D PDB for NP0290677 (6-[(3s,5r)-5-(hydroxymethyl)-1-methylpiperidin-3-yl]pyridin-2-ol)

SMILES for NP0290677 (6-[(3s,5r)-5-(hydroxymethyl)-1-methylpiperidin-3-yl]pyridin-2-ol)

INCHI for NP0290677 (6-[(3s,5r)-5-(hydroxymethyl)-1-methylpiperidin-3-yl]pyridin-2-ol)

Structure for NP0290677 (6-[(3s,5r)-5-(hydroxymethyl)-1-methylpiperidin-3-yl]pyridin-2-ol)

3D Structure for NP0290677 (6-[(3s,5r)-5-(hydroxymethyl)-1-methylpiperidin-3-yl]pyridin-2-ol)