Ligand profile

ZINC12403614

Virtual-screening candidate from ZINC.

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

Via homolog UniProt Q4K977 Formula C₁₃H₉N₃O₄
Tanimoto 0.53
Mol. weight 271.23 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC12403614
UniProt (similar protein)
Q4K977
Tanimoto
0.533
Target protein
VK055_0883

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 271.23 Da
LogP (Crippen) 3.25
H-bond donors 0
H-bond acceptors 5
TPSA 98.64 Ų
Rotatable bonds 4
Aromatic rings 2 / 2
Heavy atoms 20
Fraction sp³ C 0.00
Formula C₁₃H₉N₃O₄

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy Check

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 98.6
  • −1 ≤ LogP ≤ 5 3.25
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 271.2
  • LogP ≤ 5 3.25
  • H-bond donors ≤ 5 0
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 98.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
O=[N+]([O-])c1ccc(/C=N/c2ccc([N+](=O)[O-])cc2)cc1
InChI 
InChI=1S/C13H9N3O4/c17-15(18)12-5-1-10(2-6-12)9-14-11-3-7-13(8-4-11)16(19)20/h1-9H/b14-9+
InChIKey 
KRLIGBJKICAQHW-NTEUORMPSA-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)