IMPPAT Phytochemical information: 
5-Methylcytosine

5-Methylcytosine
Summary

SMILES: Cc1cnc(=O)[nH]c1N
InChI: InChI=1S/C5H7N3O/c1-3-2-7-5(9)8-4(3)6/h2H,1H3,(H3,6,7,8,9)
InChIKey: LRSASMSXMSNRBT-UHFFFAOYSA-N
DeepSMILES: Cccnc=O)[nH]c6N
Scaffold Graph/Node/Bond level: O=c1nccc[nH]1
Scaffold Graph/Node level: OC1NCCCN1
Scaffold Graph level: CC1CCCCC1
Functional groups: cN; cnc; c=O; c[nH]c
Chemical classification
ClassyFire Kingdom: Organic compounds
ClassyFire Superclass: Organoheterocyclic compounds
ClassyFire Class: Diazines
ClassyFire Subclass: Pyrimidines and pyrimidine derivatives
NP Classifier Biosynthetic pathway: Alkaloids
NP Classifier Superclass: Pseudoalkaloids
NP Classifier Class: pteridine alkaloids
Synonymous chemical names:
5-methylcytosine
External chemical identifiers:
CID:CID_65040; ChEBI:CHEBI:27551; ZINC:ZINC000000394712; FDASRS:6R795CQT4H; SureChEMBL:SCHEMBL22008; MolPort-004-759-608
Chemical structure download


5-Methylcytosine
Physicochemical properties
Property name Tool Property value
Molecular weight (g/mol) RDKit 125.13
Log P RDKit -0.34
Topological polar surface area (Å2) RDKit 71.77
Number of hydrogen bond acceptors RDKit 3
Number of hydrogen bond donors RDKit 2
Number of carbon atoms RDKit 5
Number of heavy atoms RDKit 9
Number of heteroatoms RDKit 4
Number of nitrogen atoms RDKit 3
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 4
Number of sp3 hybridized carbon atoms RDKit 1
Shape complexity RDKit 0.2
Number of rotatable bonds RDKit 0
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-Methylcytosine
Drug-likeness properties
Property nameToolProperty value
Number of Lipinski’s rule of 5 violations RDKit 0
Lipinski’s rule of 5 filter RDKit Passed
Number of Ghose filter violations RDKit 3
Ghose filter RDKit Failed
Veber filter RDKit Good
Pfizer 3/75 filter RDKit Bad
GSK 4/400 filter RDKit Good
Weighted quantitative estimate of drug-likeness (QEDw) score RDKit 0.497919


5-Methylcytosine
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 -7.64
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


5-Methylcytosine
Human target proteins
Protein identifierHGNC symbolCombined score from STITCH database
ENSP00000352516DNMT1773
ENSP00000362748TET1827
ENSP00000386869TET3847
ENSP00000249910MBD4707
ENSP00000369351TET2775
The human target proteins were predicted using STITCH, a database of Chemical-Protein interaction networks.