Ligand profile

JF8

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

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

Via homolog PDB 6qqu UniProt B1MDI3 Formula C₁₂H₉N₅
Mol. weight 223.24 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
JF8
PDB
6qqu
UniProt (similar protein)
B1MDI3
Target protein
KP13_02423

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 223.24 Da
LogP (Crippen) 2.01
H-bond donors 3
H-bond acceptors 3
TPSA 94.28 Ų
Rotatable bonds 1
Aromatic rings 3 / 3
Heavy atoms 17
Fraction sp³ C 0.00
Formula C₁₂H₉N₅

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy Check

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 94.3
  • −1 ≤ LogP ≤ 5 2.01
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 223.2
  • LogP ≤ 5 2.01
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 1
  • TPSA ≤ 140 Ų 94.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc(cc2c1cc[nH]2)c3c(c([nH]n3)N)C#N
InChI 
InChI=1S/C12H9N5/c13-6-9-11(16-17-12(9)14)8-2-1-7-3-4-15-10(7)5-8/h1-5,15H,(H3,14,16,17)
InChIKey 
ALVYLOVBZSBJDI-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)