Ligand profile

ZINC104039967

Virtual-screening candidate from ZINC.

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

Via homolog UniProt Q4K977 Formula C₁₂H₈N₄O₅
Tanimoto 0.62
Mol. weight 288.22 Da
Permeability Check
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC104039967
UniProt (similar protein)
Q4K977
Tanimoto
0.615
Target protein
VK055_0883

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 288.22 Da
LogP (Crippen) 3.43
H-bond donors 0
H-bond acceptors 6
TPSA 124.71 Ų
Rotatable bonds 4
Aromatic rings 2 / 2
Heavy atoms 21
Fraction sp³ C 0.00
Formula C₁₂H₈N₄O₅

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 124.7
  • −1 ≤ LogP ≤ 5 3.43
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 288.2
  • LogP ≤ 5 3.43
  • H-bond donors ≤ 5 0
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 124.7
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=[N+]([O-])c2ccc([N+](=O)[O-])cc2)cc1
InChI 
InChI=1S/C12H8N4O5/c17-14(10-5-7-12(8-6-10)16(20)21)13-9-1-3-11(4-2-9)15(18)19/h1-8H
InChIKey 
RMXNMGKOQFNSOV-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)