Ligand profile

JEH

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

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

Via homolog PDB 6qrd UniProt B1MDI3 Formula C₂₇H₃₁N₇
Mol. weight 453.59 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
JEH
PDB
6qrd
UniProt (similar protein)
B1MDI3
Target protein
KP13_02423

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 453.59 Da
LogP (Crippen) 4.06
H-bond donors 2
H-bond acceptors 6
TPSA 89.90 Ų
Rotatable bonds 6
Aromatic rings 4 / 5
Heavy atoms 34
Fraction sp³ C 0.33
Formula C₂₇H₃₁N₇

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 89.9
  • −1 ≤ LogP ≤ 5 4.06
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 453.6
  • LogP ≤ 5 4.06
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 89.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(C)N1CCN(CC1)Cc2ccc(cc2)Cn3ccc4c3cc(cc4)c5c(c([nH]n5)N)C#N
InChI 
InChI=1S/C27H31N7/c1-19(2)33-13-11-32(12-14-33)17-20-3-5-21(6-4-20)18-34-10-9-22-7-8-23(15-25(22)34)26-24(16-28)27(29)31-30-26/h3-10,15,19H,11-14,17-18H2,1-2H3,(H3,29,30,31)
InChIKey 
ZLJXHHAUABPXJM-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)