Ligand profile

JCZ

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

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

Via homolog PDB 6qqs UniProt B1MDI3 Formula C₁₁H₁₀N₄
Mol. weight 198.23 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
JCZ
PDB
6qqs
UniProt (similar protein)
B1MDI3
Target protein
KP13_02423

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 198.23 Da
LogP (Crippen) 2.14
H-bond donors 3
H-bond acceptors 2
TPSA 70.49 Ų
Rotatable bonds 1
Aromatic rings 3 / 3
Heavy atoms 15
Fraction sp³ C 0.00
Formula C₁₁H₁₀N₄

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 70.5
  • −1 ≤ LogP ≤ 5 2.14
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 198.2
  • LogP ≤ 5 2.14
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 2
Veber's rules Pass
  • Rotatable bonds ≤ 10 1
  • TPSA ≤ 140 Ų 70.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc(cc2c1cc[nH]2)c3cc([nH]n3)N
InChI 
InChI=1S/C11H10N4/c12-11-6-10(14-15-11)8-2-1-7-3-4-13-9(7)5-8/h1-6,13H,(H3,12,14,15)
InChIKey 
WGNBSWSUVHVDSW-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)