Ligand profile

ZINC100456108

Virtual-screening candidate from ZINC.

Bound to: VK055_2653 — 3,4-dihydroxyphenylacetate 2,3-dioxygenase

Via homolog UniProt Q6J1Z6 Formula C₁₃H₉N₃O₅
Tanimoto 0.53
Mol. weight 287.23 Da
Permeability Check
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC100456108
UniProt (similar protein)
Q6J1Z6
Tanimoto
0.529
Target protein
VK055_2653

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 287.23 Da
LogP (Crippen) 2.96
H-bond donors 1
H-bond acceptors 6
TPSA 118.87 Ų
Rotatable bonds 4
Aromatic rings 2 / 2
Heavy atoms 21
Fraction sp³ C 0.00
Formula C₁₃H₉N₃O₅

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 118.9
  • −1 ≤ LogP ≤ 5 2.96
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 287.2
  • LogP ≤ 5 2.96
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 118.9
PAINS Alert

Matches PAINS filter: imine_phenol_A(3). May be a frequent false positive in HTS — review carefully.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
O=[N+]([O-])c1ccc(/C=N/c2ccc([N+](=O)[O-])cc2O)cc1
InChI 
InChI=1S/C13H9N3O5/c17-13-7-11(16(20)21)5-6-12(13)14-8-9-1-3-10(4-2-9)15(18)19/h1-8,17H/b14-8+
InChIKey 
GNDQTJIKKPHGTI-RIYZIHGNSA-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
Q6J1Z6

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_2653.

PDB 3

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)