Ligand profile

ZINC104075553

Virtual-screening candidate from ZINC.

Bound to: VK055_0883 — bacterial regulatory helix-turn-helix, AraC family protein

Via homolog UniProt Q4K977 Formula C₁₂H₉N₃O₃
Tanimoto 0.50
Mol. weight 243.22 Da
Permeability High
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC104075553
UniProt (similar protein)
Q4K977
Tanimoto
0.500
Target protein
VK055_0883

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 243.22 Da
LogP (Crippen) 3.52
H-bond donors 0
H-bond acceptors 4
TPSA 81.57 Ų
Rotatable bonds 3
Aromatic rings 2 / 2
Heavy atoms 18
Fraction sp³ C 0.00
Formula C₁₂H₉N₃O₃

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 81.6
  • −1 ≤ LogP ≤ 5 3.52
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 243.2
  • LogP ≤ 5 3.52
  • H-bond donors ≤ 5 0
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 81.6
PAINS Alert

Matches PAINS filter: azo_A(324). May be a frequent false positive in HTS — review carefully.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
O=[N+]([O-])c1ccc([N+]([O-])=Nc2ccccc2)cc1
InChI 
InChI=1S/C12H9N3O3/c16-14(13-10-4-2-1-3-5-10)11-6-8-12(9-7-11)15(17)18/h1-9H
InChIKey 
AYTMBPVOPZZDCM-UHFFFAOYSA-N

Provenance

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

Method
LigQ nearest_k
Query
QCV
Homolog
Q4K977

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_0883.

PDB 2

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

Ligand PDB entry

ZINC 49

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)