Ligand profile

9D0

Bioactivity hit from ChEMBL on a similar protein.

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

Via homolog UniProt Q9HXQ1 Formula C₂₃H₃₀N₄O₂S
pchembl 8.80 ~1.6 nM
Mol. weight 426.59 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
9D0
UniProt (similar protein)
Q9HXQ1
pchembl
8.800 (~1.6 nM)
Target protein
KP13_02423

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 426.59 Da
LogP (Crippen) 4.36
H-bond donors 3
H-bond acceptors 5
TPSA 86.88 Ų
Rotatable bonds 12
Aromatic rings 3 / 3
Heavy atoms 30
Fraction sp³ C 0.43
Formula C₂₃H₃₀N₄O₂S

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 4.36
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 426.6
  • LogP ≤ 5 4.36
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 5
Veber's rules Fail
  • Rotatable bonds ≤ 10 12
  • TPSA ≤ 140 Ų 86.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCCCCCCCNCc1ccc(cc1)CNC(=O)c2csc3c2C(=O)NC=N3
InChI 
InChI=1S/C23H30N4O2S/c1-2-3-4-5-6-7-12-24-13-17-8-10-18(11-9-17)14-25-21(28)19-15-30-23-20(19)22(29)26-16-27-23/h8-11,15-16,24H,2-7,12-14H2,1H3,(H,25,28)(H,26,27,29)
InChIKey 
SZWXXUKSELBLQK-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)