Ligand profile

CHEMBL4584637

Bioactivity hit from ChEMBL on a similar protein.

Bound to: KP13_02423 — tRNA (guanine-N(1)-)-methyltransferase

Via homolog UniProt Q9HXQ1 Formula C₂₁H₂₄N₄O₂S
pchembl 6.10 ~794.3 nM
Mol. weight 396.52 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL4584637
UniProt (similar protein)
Q9HXQ1
pchembl
6.100 (~794.3 nM)
Target protein
KP13_02423

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 396.52 Da
LogP (Crippen) 3.34
H-bond donors 3
H-bond acceptors 5
TPSA 86.88 Ų
Rotatable bonds 6
Aromatic rings 3 / 4
Heavy atoms 28
Fraction sp³ C 0.38
Formula C₂₁H₂₄N₄O₂S

Drug-likeness

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

Permeability proxy High

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 86.9
  • −1 ≤ LogP ≤ 5 3.34
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 396.5
  • LogP ≤ 5 3.34
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 86.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
O=C(NCc1ccc(CNC2CCCCC2)cc1)c1csc2nc[nH]c(=O)c12
InChI 
InChI=1S/C21H24N4O2S/c26-19(17-12-28-21-18(17)20(27)24-13-25-21)23-11-15-8-6-14(7-9-15)10-22-16-4-2-1-3-5-16/h6-9,12-13,16,22H,1-5,10-11H2,(H,23,26)(H,24,25,27)
InChIKey 
JMPWESYLZQOOPK-UHFFFAOYSA-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
Binding sites
PF01746

External resources

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

Other ligands for this protein

Quick navigation to other ligands bound to KP13_02423.

PDB 89

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

Ligand PDB entry

ChEMBL 37

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)