Binder profile

JPY

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

Bound to: PA3686 — adenylate kinase

Via homolog PDB 3x2s UniProt A0A0J9X1X4 C19H15NO
Mol. weight 273.33 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
JPY
PDB
3x2s
UniProt (similar protein)
A0A0J9X1X4
Target protein
PA3686

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 273.33 Da
LogP (Crippen) 4.22
H-bond donors 1
H-bond acceptors 1
TPSA 29.10 Ų
Rotatable bonds 2
Aromatic rings 4 / 4
Heavy atoms 21
Fraction sp³ C 0.11
Formula C19H15NO

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.

Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 273.3
  • LogP ≤ 5 4.22
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 1
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 29.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(=O)NCc1ccc2ccc3cccc4c3c2c1cc4
InChI 
InChI=1S/C19H15NO/c1-12(21)20-11-16-8-7-15-6-5-13-3-2-4-14-9-10-17(16)19(15)18(13)14/h2-10H,11H2,1H3,(H,20,21)
InChIKey 
IGDIETIXWIPXQF-UHFFFAOYSA-N

Provenance

Annotation context from LigQ_2, the internal TPW step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ nearest_k
Source
PDB
Binding sites
PF00406' 'PF05191

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other binders for this protein

Quick navigation to other ligands bound to PA3686.

PDB 4

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ChEMBL 1

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)