Ligand profile

JE8

Ligand co-crystallized with a similar protein (Protein Data Bank).

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

Via homolog PDB 6qr3 UniProt B1MDI3 Formula C₁₉H₂₂N₆
Mol. weight 334.43 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
JE8
PDB
6qr3
UniProt (similar protein)
B1MDI3
Target protein
KP13_02423

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 334.43 Da
LogP (Crippen) 2.83
H-bond donors 2
H-bond acceptors 5
TPSA 86.66 Ų
Rotatable bonds 3
Aromatic rings 3 / 4
Heavy atoms 25
Fraction sp³ C 0.37
Formula C₁₉H₂₂N₆

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 86.7
  • −1 ≤ LogP ≤ 5 2.83
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 334.4
  • LogP ≤ 5 2.83
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 86.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CN1CCCC(C1)Cn2ccc3c2cc(cc3)c4c(c([nH]n4)N)C#N
InChI 
InChI=1S/C19H22N6/c1-24-7-2-3-13(11-24)12-25-8-6-14-4-5-15(9-17(14)25)18-16(10-20)19(21)23-22-18/h4-6,8-9,13H,2-3,7,11-12H2,1H3,(H3,21,22,23)
InChIKey 
AJRDTQMINSKQOE-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
PDB
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 88

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

Ligand PDB entry

ChEMBL 38

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)