Ligand profile

9D6

Bioactivity hit from ChEMBL on a similar protein.

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

Via homolog UniProt Q9HXQ1 Formula C₂₃H₂₈N₄O₂S
pchembl 6.31 ~489.8 nM
Mol. weight 424.57 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
9D6
UniProt (similar protein)
Q9HXQ1
pchembl
6.310 (~489.8 nM)
Target protein
KP13_02423

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 424.57 Da
LogP (Crippen) 4.07
H-bond donors 2
H-bond acceptors 5
TPSA 78.09 Ų
Rotatable bonds 7
Aromatic rings 3 / 4
Heavy atoms 30
Fraction sp³ C 0.43
Formula C₂₃H₂₈N₄O₂S

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 4.07
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 424.6
  • LogP ≤ 5 4.07
  • 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(Cc1ccc(cc1)CNC(=O)c2csc3c2C(=O)NC=N3)C4CCCCC4
InChI 
InChI=1S/C23H28N4O2S/c1-2-27(18-6-4-3-5-7-18)13-17-10-8-16(9-11-17)12-24-21(28)19-14-30-23-20(19)22(29)25-15-26-23/h8-11,14-15,18H,2-7,12-13H2,1H3,(H,24,28)(H,25,26,29)
InChIKey 
VDWQEXVBMIBDPI-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)