Ligand profile

CHEMBL4580116

Bioactivity hit from ChEMBL on a similar protein.

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

Via homolog UniProt Q9HXQ1 Formula C₂₂H₂₀N₄O₂S
pchembl 6.89 ~128.8 nM
Mol. weight 404.50 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL4580116
UniProt (similar protein)
Q9HXQ1
pchembl
6.890 (~128.8 nM)
Target protein
KP13_02423

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 404.50 Da
LogP (Crippen) 3.20
H-bond donors 3
H-bond acceptors 5
TPSA 86.88 Ų
Rotatable bonds 7
Aromatic rings 4 / 4
Heavy atoms 29
Fraction sp³ C 0.14
Formula C₂₂H₂₀N₄O₂S

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 3.20
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 404.5
  • LogP ≤ 5 3.20
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 86.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
O=C(NCc1ccc(CNCc2ccccc2)cc1)c1csc2nc[nH]c(=O)c12
InChI 
InChI=1S/C22H20N4O2S/c27-20(18-13-29-22-19(18)21(28)25-14-26-22)24-12-17-8-6-16(7-9-17)11-23-10-15-4-2-1-3-5-15/h1-9,13-14,23H,10-12H2,(H,24,27)(H,25,26,28)
InChIKey 
YWZMXLOFPKXASQ-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)