Ligand profile

ZINC96068546

Virtual-screening candidate from ZINC.

Bound to: VK055_0529 — protocatechuate 3,4-dioxygenase, alpha subunit

Via homolog UniProt P20371 Formula C₁₂H₉N₃O₄
Tanimoto 0.63
Mol. weight 259.22 Da
Permeability Check
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC96068546
UniProt (similar protein)
P20371
Tanimoto
0.633
Target protein
VK055_0529

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 259.22 Da
LogP (Crippen) 3.42
H-bond donors 2
H-bond acceptors 6
TPSA 108.32 Ų
Rotatable bonds 3
Aromatic rings 2 / 2
Heavy atoms 19
Fraction sp³ C 0.00
Formula C₁₂H₉N₃O₄

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 108.3
  • −1 ≤ LogP ≤ 5 3.42
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 259.2
  • LogP ≤ 5 3.42
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 108.3
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=Nc2ccc(O)c(O)c2)cc1
InChI 
InChI=1S/C12H9N3O4/c16-11-6-3-9(7-12(11)17)14-13-8-1-4-10(5-2-8)15(18)19/h1-7,16-17H
InChIKey 
DGOZWUSVOBKXNR-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
4NC
Homolog
P20371

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_0529.

PDB 17

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)