IMPPAT Phytochemical information: 
5-(Hydroxymethyl)-4-(methoxymethyl)-2-methylpyridin-3-ol

5-(Hydroxymethyl)-4-(methoxymethyl)-2-methylpyridin-3-ol
Summary

SMILES: COCc1c(CO)cnc(c1O)C
InChI: InChI=1S/C9H13NO3/c1-6-9(12)8(5-13-2)7(4-11)3-10-6/h3,11-12H,4-5H2,1-2H3
InChIKey: SVINQHQHARVZFF-UHFFFAOYSA-N
DeepSMILES: COCccCO))cncc6O))C
Scaffold Graph/Node/Bond level: c1ccncc1
Scaffold Graph/Node level: C1CCNCC1
Scaffold Graph level: C1CCCCC1
Functional groups: cnc; COC; cO; CO
Chemical classification
ClassyFire Kingdom: Organic compounds
ClassyFire Superclass: Organoheterocyclic compounds
ClassyFire Class: Pyridines and derivatives
ClassyFire Subclass: Pyridoxines
NP Classifier Biosynthetic pathway: Alkaloids
NP Classifier Superclass: Nicotinic acid alkaloids
NP Classifier Class: Pyridine alkaloids
Synonymous chemical names:
ginkgotoxin
External chemical identifiers:
CID:CID_76581; ChEMBL:CHEMBL1076875; ChEBI:CHEBI:166575; ZINC:ZINC000011535715; SureChEMBL:SCHEMBL9127650
Chemical structure download


5-(Hydroxymethyl)-4-(methoxymethyl)-2-methylpyridin-3-ol
Physicochemical properties
Property name Tool Property value
Molecular weight (g/mol) RDKit 183.21
Log P RDKit 0.73
Topological polar surface area (Å2) RDKit 62.58
Number of hydrogen bond acceptors RDKit 4
Number of hydrogen bond donors RDKit 2
Number of carbon atoms RDKit 9
Number of heavy atoms RDKit 13
Number of heteroatoms RDKit 4
Number of nitrogen atoms RDKit 1
Number of sulfur atoms RDKit 0
Number of chiral carbon atoms RDKit 0
Stereochemical complexity RDKit 0
Number of sp hybridized carbon atoms RDKit 0
Number of sp2 hybridized carbon atoms RDKit 5
Number of sp3 hybridized carbon atoms RDKit 4
Shape complexity RDKit 0.44
Number of rotatable bonds RDKit 3
Number of aliphatic carbocycles RDKit 0
Number of aliphatic heterocycles RDKit 0
Number of aliphatic rings RDKit 0
Number of aromatic carbocycles RDKit 0
Number of aromatic heterocycles RDKit 1
Number of aromatic rings RDKit 1
Total number of rings RDKit 1
Number of saturated carbocycles RDKit 0
Number of saturated heterocycles RDKit 0
Number of saturated rings RDKit 0
Number of Smallest Set of Smallest Rings (SSSR) RDKit 1


5-(Hydroxymethyl)-4-(methoxymethyl)-2-methylpyridin-3-ol
Drug-likeness properties
Property nameToolProperty value
Number of Lipinski’s rule of 5 violations RDKit 0
Lipinski’s rule of 5 RDKit Passed
Number of Ghose rule violations RDKit 0
Ghose rule RDKit Passed
Veber rule RDKit Good
Egan rule RDKit Good
GSK 4/400 rule RDKit Good
Pfizer 3/75 rule RDKit Bad
Weighted quantitative estimate of drug-likeness (QEDw) score RDKit 0.72


5-(Hydroxymethyl)-4-(methoxymethyl)-2-methylpyridin-3-ol
ADME properties
Property nameToolProperty value
Bioavailability score SwissADME 0.55
Solubility class [ESOL] SwissADME Very soluble
Solubility class [Silicos-IT] SwissADME Soluble
Blood Brain Barrier permeation SwissADME No
Gastrointestinal absorption SwissADME High
Log Kp (Skin permeation, cm/s) SwissADME -7.35
Number of PAINS structural alerts SwissADME 0
Number of Brenk structural alerts SwissADME 0
CYP1A2 inhibitor SwissADME No
CYP2C19 inhibitor SwissADME No
CYP2C9 inhibitor SwissADME No
CYP2D6 inhibitor SwissADME No
CYP3A4 inhibitor SwissADME No
P-glycoprotein substrate SwissADME No