Ligand profile

JB5

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

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

Via homolog PDB 6qol UniProt B1MDI3 Formula C₈H₇N₃
Mol. weight 145.17 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
JB5
PDB
6qol
UniProt (similar protein)
B1MDI3
Target protein
KP13_02423

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 145.17 Da
LogP (Crippen) 1.21
H-bond donors 1
H-bond acceptors 3
TPSA 51.80 Ų
Rotatable bonds 0
Aromatic rings 2 / 2
Heavy atoms 11
Fraction sp³ C 0.00
Formula C₈H₇N₃

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 51.8
  • −1 ≤ LogP ≤ 5 1.21
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 145.2
  • LogP ≤ 5 1.21
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 0
  • TPSA ≤ 140 Ų 51.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc2c(cc1N)nccn2
InChI 
InChI=1S/C8H7N3/c9-6-1-2-7-8(5-6)11-4-3-10-7/h1-5H,9H2
InChIKey 
MSGRFBKVMUKEGZ-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)