NP-MRD: Showing NP-Card for 2-(1-{7-hydroxy-9a,11a-dimethyl-1h,2h,3h,3ah,3bh,4h,6h,7h,8h,9h,9bh,10h,11h-cyclopenta[a]phenanthren-1-yl}ethyl)-5-methylpyridin-3-ol (NP0249152)

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Record Information

Version

2.0

Created at

2022-09-07 11:38:07 UTC

Updated at

2022-09-07 11:38:07 UTC

NP-MRD ID

NP0249152

Secondary Accession Numbers

None

Natural Product Identification

Common Name

2-(1-{7-hydroxy-9a,11a-dimethyl-1h,2h,3h,3ah,3bh,4h,6h,7h,8h,9h,9bh,10h,11h-cyclopenta[a]phenanthren-1-yl}ethyl)-5-methylpyridin-3-ol

Description

2-(1-{5-Hydroxy-2,15-dimethyltetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]Heptadec-7-en-14-yl}ethyl)-5-methylpyridin-3-ol belongs to the class of organic compounds known as gluco/mineralocorticoids, progestogins and derivatives. These are steroids with a structure based on a hydroxylated prostane moiety. 2-(1-{7-hydroxy-9a,11a-dimethyl-1h,2h,3h,3ah,3bh,4h,6h,7h,8h,9h,9bh,10h,11h-cyclopenta[a]phenanthren-1-yl}ethyl)-5-methylpyridin-3-ol is found in Eclipta alba. 2-(1-{5-Hydroxy-2,15-dimethyltetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]Heptadec-7-en-14-yl}ethyl)-5-methylpyridin-3-ol is a very strong basic compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1533004191520162D          

 30 34  0  0  0  0            999 V2000
    2.8728   -3.9050    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5619   -3.1408    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0683   -2.4895    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8390   -1.6970    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5218   -1.2340    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1731   -1.7404    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9853   -1.5952    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2655   -0.8192    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0777   -0.6740    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6095   -1.3047    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.4216   -1.1595    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.9534   -1.7902    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.7655   -1.6450    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.6731   -2.5662    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8610   -2.7114    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3292   -2.0807    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0489   -2.8566    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5171   -2.2259    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2368   -3.0018    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4247   -3.1470    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8928   -2.5163    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5330   -3.2587    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7447   -3.0280    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2383   -3.6793    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.4211   -3.5665    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1102   -2.8023    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7071   -2.6894    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    1.9401   -1.6125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
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  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
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 10 16  1  0  0  0  0
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  7 18  1  0  0  0  0
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  3 21  1  0  0  0  0
  6 21  1  0  0  0  0
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 26 28  1  0  0  0  0
 28 29  2  0  0  0  0
 23 29  1  0  0  0  0
 29 30  1  0  0  0  0
M  END

     RDKit          3D

 69 73  0  0  0  0  0  0  0  0999 V2000
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M  END


  Mrv1533004191520162D          

 30 34  0  0  0  0            999 V2000
    2.8728   -3.9050    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5619   -3.1408    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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 29 30  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0249152

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C1CCC2C3CC=C4CC(O)CCC4(C)C3CCC12C)C1=NC=C(C)C=C1O

> <INCHI_IDENTIFIER>
InChI=1S/C27H39NO2/c1-16-13-24(30)25(28-15-16)17(2)21-7-8-22-20-6-5-18-14-19(29)9-11-26(18,3)23(20)10-12-27(21,22)4/h5,13,15,17,19-23,29-30H,6-12,14H2,1-4H3

> <INCHI_KEY>
RODDEOSIMRCKKR-UHFFFAOYSA-N

> <FORMULA>
C27H39NO2

> <MOLECULAR_WEIGHT>
409.614

> <EXACT_MASS>
409.2980795

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
69

> <JCHEM_AVERAGE_POLARIZABILITY>
49.49838929378495

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
2-(1-{5-hydroxy-2,15-dimethyltetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadec-7-en-14-yl}ethyl)-5-methylpyridin-3-ol

> <ALOGPS_LOGP>
5.74

> <JCHEM_LOGP>
5.303466031333333

> <ALOGPS_LOGS>
-5.43

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
18.20428950550382

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.85789958833086

> <JCHEM_PKA_STRONGEST_BASIC>
6.127086208432361

> <JCHEM_POLAR_SURFACE_AREA>
53.35000000000001

> <JCHEM_REFRACTIVITY>
122.22619999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.53e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-(1-{5-hydroxy-2,15-dimethyltetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadec-7-en-14-yl}ethyl)-5-methylpyridin-3-ol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 19-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   19-APR-15         0                                  
HETATM    1  C   UNK     0       5.363  -7.289   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.782  -5.863   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.727  -4.647   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.299  -3.168   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       6.574  -2.304   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       7.790  -3.249   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       9.306  -2.978   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       9.829  -1.529   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      11.345  -1.258   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      12.338  -2.436   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      13.854  -2.164   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      14.846  -3.342   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      16.362  -3.071   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0      14.323  -4.790   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      12.807  -5.061   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      11.814  -3.884   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      11.291  -5.332   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      10.299  -4.155   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       9.775  -5.603   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       8.259  -5.874   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       7.267  -4.697   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       6.595  -6.083   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       3.257  -5.652   0.000  0.00  0.00           C+0
HETATM   24  N   UNK     0       2.312  -6.868   0.000  0.00  0.00           N+0
HETATM   25  C   UNK     0       0.786  -6.657   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       0.206  -5.231   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      -1.320  -5.020   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       1.151  -4.015   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       2.676  -4.226   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0       3.622  -3.010   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   23                                                  
CONECT    3    2    4   21                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7   21                                                  
CONECT    7    6    8   18                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11   16                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   10   17   18                                             
CONECT   17   16                                                            
CONECT   18   16    7   19                                                  
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20    3    6   22                                             
CONECT   22   21                                                            
CONECT   23    2   24   29                                                  
CONECT   24   23   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27   28                                                  
CONECT   27   26                                                            
CONECT   28   26   29                                                       
CONECT   29   28   23   30                                                  
CONECT   30   29                                                            
MASTER        0    0    0    0    0    0    0    0   30    0   68    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₇H₃₉NO₂

Average Mass

409.6140 Da

Monoisotopic Mass

409.29808 Da

IUPAC Name

2-(1-{5-hydroxy-2,15-dimethyltetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadec-7-en-14-yl}ethyl)-5-methylpyridin-3-ol

Traditional Name

2-(1-{5-hydroxy-2,15-dimethyltetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadec-7-en-14-yl}ethyl)-5-methylpyridin-3-ol

CAS Registry Number

Not Available

SMILES

CC(C1CCC2C3CC=C4CC(O)CCC4(C)C3CCC12C)C1=NC=C(C)C=C1O

InChI Identifier

InChI=1S/C27H39NO2/c1-16-13-24(30)25(28-15-16)17(2)21-7-8-22-20-6-5-18-14-19(29)9-11-26(18,3)23(20)10-12-27(21,22)4/h5,13,15,17,19-23,29-30H,6-12,14H2,1-4H3

InChI Key

RODDEOSIMRCKKR-UHFFFAOYSA-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
Eclipta alba	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as gluco/mineralocorticoids, progestogins and derivatives. These are steroids with a structure based on a hydroxylated prostane moiety.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Steroids and steroid derivatives

Sub Class

Pregnane steroids

Direct Parent

Gluco/mineralocorticoids, progestogins and derivatives

Alternative Parents

Substituents

Progestogin-skeleton
3-hydroxy-delta-5-steroid
3-hydroxysteroid
Hydroxysteroid
Delta-5-steroid
Methylpyridine
Hydroxypyridine
Pyridine
Heteroaromatic compound
Cyclic alcohol
Secondary alcohol
Organoheterocyclic compound
Azacycle
Organic nitrogen compound
Organooxygen compound
Organonitrogen compound
Hydrocarbon derivative
Organopnictogen compound
Alcohol
Organic oxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic 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
logP	5.74	ALOGPS
logP	5.3	ChemAxon
logS	-5.4	ALOGPS
pKa (Strongest Acidic)	9.86	ChemAxon
pKa (Strongest Basic)	6.13	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	53.35 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	122.23 m³·mol⁻¹	ChemAxon
Polarizability	49.5 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 2-(1-{7-hydroxy-9a,11a-dimethyl-1h,2h,3h,3ah,3bh,4h,6h,7h,8h,9h,9bh,10h,11h-cyclopenta[a]phenanthren-1-yl}ethyl)-5-methylpyridin-3-ol (NP0249152)

MOL for NP0249152 (2-(1-{7-hydroxy-9a,11a-dimethyl-1h,2h,3h,3ah,3bh,4h,6h,7h,8h,9h,9bh,10h,11h-cyclopenta[a]phenanthren-1-yl}ethyl)-5-methylpyridin-3-ol)

3D MOL for NP0249152 (2-(1-{7-hydroxy-9a,11a-dimethyl-1h,2h,3h,3ah,3bh,4h,6h,7h,8h,9h,9bh,10h,11h-cyclopenta[a]phenanthren-1-yl}ethyl)-5-methylpyridin-3-ol)

3D SDF for NP0249152 (2-(1-{7-hydroxy-9a,11a-dimethyl-1h,2h,3h,3ah,3bh,4h,6h,7h,8h,9h,9bh,10h,11h-cyclopenta[a]phenanthren-1-yl}ethyl)-5-methylpyridin-3-ol)

3D-SDF for NP0249152 (2-(1-{7-hydroxy-9a,11a-dimethyl-1h,2h,3h,3ah,3bh,4h,6h,7h,8h,9h,9bh,10h,11h-cyclopenta[a]phenanthren-1-yl}ethyl)-5-methylpyridin-3-ol)

PDB for NP0249152 (2-(1-{7-hydroxy-9a,11a-dimethyl-1h,2h,3h,3ah,3bh,4h,6h,7h,8h,9h,9bh,10h,11h-cyclopenta[a]phenanthren-1-yl}ethyl)-5-methylpyridin-3-ol)

3D PDB for NP0249152 (2-(1-{7-hydroxy-9a,11a-dimethyl-1h,2h,3h,3ah,3bh,4h,6h,7h,8h,9h,9bh,10h,11h-cyclopenta[a]phenanthren-1-yl}ethyl)-5-methylpyridin-3-ol)

SMILES for NP0249152 (2-(1-{7-hydroxy-9a,11a-dimethyl-1h,2h,3h,3ah,3bh,4h,6h,7h,8h,9h,9bh,10h,11h-cyclopenta[a]phenanthren-1-yl}ethyl)-5-methylpyridin-3-ol)

INCHI for NP0249152 (2-(1-{7-hydroxy-9a,11a-dimethyl-1h,2h,3h,3ah,3bh,4h,6h,7h,8h,9h,9bh,10h,11h-cyclopenta[a]phenanthren-1-yl}ethyl)-5-methylpyridin-3-ol)

Structure for NP0249152 (2-(1-{7-hydroxy-9a,11a-dimethyl-1h,2h,3h,3ah,3bh,4h,6h,7h,8h,9h,9bh,10h,11h-cyclopenta[a]phenanthren-1-yl}ethyl)-5-methylpyridin-3-ol)

3D Structure for NP0249152 (2-(1-{7-hydroxy-9a,11a-dimethyl-1h,2h,3h,3ah,3bh,4h,6h,7h,8h,9h,9bh,10h,11h-cyclopenta[a]phenanthren-1-yl}ethyl)-5-methylpyridin-3-ol)