Ligand profile

CHEMBL4588797

Bioactivity hit from ChEMBL on a similar protein.

Bound to: VK055_0016 — cytosine-specific methyltransferase

Via homolog UniProt P26358 Formula C₁₆H₂₀N₆O₅S
pchembl 6.82 ~151.4 nM
Mol. weight 408.44 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL4588797
UniProt (similar protein)
P26358
pchembl
6.820 (~151.4 nM)
Target protein
VK055_0016

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 408.44 Da
LogP (Crippen) -0.96
H-bond donors 5
H-bond acceptors 11
TPSA 193.53 Ų
Rotatable bonds 7
Aromatic rings 2 / 3
Heavy atoms 28
Fraction sp³ C 0.50
Formula C₁₆H₂₀N₆O₅S

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy Check

Estimated from TPSA and LogP only: TPSA ≤ 90 Ų and −1 ≤ LogP ≤ 5 are treated as a favorable small-molecule permeability screen.

  • TPSA ≤ 90 Ų 193.5
  • −1 ≤ LogP ≤ 5 -0.96
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 408.4
  • LogP ≤ 5 -0.96
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 11
Veber's rules Fail
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 193.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
N#Cc1cn([C@@H]2O[C@H](CSCC[C@H](N)C(=O)O)[C@@H](O)[C@H]2O)c2ncnc(N)c12
InChI 
InChI=1S/C16H20N6O5S/c17-3-7-4-22(14-10(7)13(19)20-6-21-14)15-12(24)11(23)9(27-15)5-28-2-1-8(18)16(25)26/h4,6,8-9,11-12,15,23-24H,1-2,5,18H2,(H,25,26)(H2,19,20,21)/t8-,9+,11+,12+,15+/m0/s1
InChIKey 
XLTWYAYAFLGUEQ-OPYVMVOTSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ nearest_k
Source
ChEMBL
Curation
pdb_similarity_tanimoto
Binding sites
PF00145

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to VK055_0016.

PDB 3

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ChEMBL 13

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 50

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)