Ligand profile

JFE

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

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

Via homolog PDB 6qrc UniProt B1MDI3 Formula C₁₉H₁₈N₄O
Mol. weight 318.38 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
JFE
PDB
6qrc
UniProt (similar protein)
B1MDI3
Target protein
KP13_02423

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 318.38 Da
LogP (Crippen) 3.67
H-bond donors 2
H-bond acceptors 4
TPSA 68.86 Ų
Rotatable bonds 4
Aromatic rings 4 / 4
Heavy atoms 24
Fraction sp³ C 0.11
Formula C₁₉H₁₈N₄O

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 68.9
  • −1 ≤ LogP ≤ 5 3.67
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 318.4
  • LogP ≤ 5 3.67
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 68.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
COc1cccc(c1)Cn2ccc3c2cc(cc3)c4cc([nH]n4)N
InChI 
InChI=1S/C19H18N4O/c1-24-16-4-2-3-13(9-16)12-23-8-7-14-5-6-15(10-18(14)23)17-11-19(20)22-21-17/h2-11H,12H2,1H3,(H3,20,21,22)
InChIKey 
HOUGYQANDNDSLX-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)