Ligand profile

JEQ

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

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

Via homolog PDB 6qrb UniProt B1MDI3 Formula C₂₅H₂₆N₆
Mol. weight 410.53 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
JEQ
PDB
6qrb
UniProt (similar protein)
B1MDI3
Target protein
KP13_02423

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 410.53 Da
LogP (Crippen) 4.40
H-bond donors 2
H-bond acceptors 5
TPSA 86.66 Ų
Rotatable bonds 5
Aromatic rings 4 / 5
Heavy atoms 31
Fraction sp³ C 0.28
Formula C₂₅H₂₆N₆

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 4.40
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 410.5
  • LogP ≤ 5 4.40
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 86.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1ccc(cc1)CN2CCCC(C2)Cn3ccc4c3cc(cc4)c5c(c([nH]n5)N)C#N
InChI 
InChI=1S/C25H26N6/c26-14-22-24(28-29-25(22)27)21-9-8-20-10-12-31(23(20)13-21)17-19-7-4-11-30(16-19)15-18-5-2-1-3-6-18/h1-3,5-6,8-10,12-13,19H,4,7,11,15-17H2,(H3,27,28,29)
InChIKey 
RLAAKYCZJLWQDL-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)