Ligand profile

9D3

Bioactivity hit from ChEMBL on a similar protein.

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

Via homolog UniProt Q9HXQ1 Formula C₁₉H₂₂N₄O₂S
pchembl 6.14 ~724.4 nM
Mol. weight 370.48 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
9D3
UniProt (similar protein)
Q9HXQ1
pchembl
6.140 (~724.4 nM)
Target protein
KP13_02423

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 370.48 Da
LogP (Crippen) 2.76
H-bond donors 2
H-bond acceptors 5
TPSA 78.09 Ų
Rotatable bonds 7
Aromatic rings 3 / 3
Heavy atoms 26
Fraction sp³ C 0.32
Formula C₁₉H₂₂N₄O₂S

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 78.1
  • −1 ≤ LogP ≤ 5 2.76
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 370.5
  • LogP ≤ 5 2.76
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 78.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCN(CC)Cc1ccc(cc1)CNC(=O)c2csc3c2C(=O)NC=N3
InChI 
InChI=1S/C19H22N4O2S/c1-3-23(4-2)10-14-7-5-13(6-8-14)9-20-17(24)15-11-26-19-16(15)18(25)21-12-22-19/h5-8,11-12H,3-4,9-10H2,1-2H3,(H,20,24)(H,21,22,25)
InChIKey 
SNPTXDKRQKLKGA-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)