Ligand profile

JFH

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

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

Via homolog PDB 6qr5 UniProt B1MDI3 Formula C₂₃H₂₅N₅
Mol. weight 371.49 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
JFH
PDB
6qr5
UniProt (similar protein)
B1MDI3
Target protein
KP13_02423

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 371.49 Da
LogP (Crippen) 4.26
H-bond donors 2
H-bond acceptors 4
TPSA 62.87 Ų
Rotatable bonds 5
Aromatic rings 4 / 5
Heavy atoms 28
Fraction sp³ C 0.26
Formula C₂₃H₂₅N₅

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 62.9
  • −1 ≤ LogP ≤ 5 4.26
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 371.5
  • LogP ≤ 5 4.26
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 62.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc(ccc1Cn2ccc3c2cc(cc3)c4cc([nH]n4)N)CN5CCCC5
InChI 
InChI=1S/C23H25N5/c24-23-14-21(25-26-23)20-8-7-19-9-12-28(22(19)13-20)16-18-5-3-17(4-6-18)15-27-10-1-2-11-27/h3-9,12-14H,1-2,10-11,15-16H2,(H3,24,25,26)
InChIKey 
QHKSDDZUHNXXME-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)