Ligand profile

JPY

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

Bound to: VK055_2093 — adenylate kinase

Via homolog PDB 3x2s UniProt A0A0J9X1X4 Formula 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
VK055_2093

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.

  • TPSA ≤ 90 Ų 29.1
  • −1 ≤ LogP ≤ 5 4.22
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 Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ sequence
Source
PDB
Binding sites
PF00406' 'PF05191

External resources

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

Other ligands for this protein

Quick navigation to other ligands bound to VK055_2093.

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)