Ligand profile

16N

Ligand co-crystallized with a similar protein (Protein Data Bank).

Bound to: VK055_0611 — 2-halobenzoate 1,2-dioxygenase large subunit

Via homolog PDB 4hm4 UniProt P0A111 Formula C₉H₁₀
Mol. weight 118.18 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
16N
PDB
4hm4
UniProt (similar protein)
P0A111
Target protein
VK055_0611

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 118.18 Da
LogP (Crippen) 2.18
H-bond donors 0
H-bond acceptors 0
TPSA 0.00 Ų
Rotatable bonds 0
Aromatic rings 1 / 2
Heavy atoms 9
Fraction sp³ C 0.33
Formula C₉H₁₀

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 0.0
  • −1 ≤ LogP ≤ 5 2.18
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 118.2
  • LogP ≤ 5 2.18
  • H-bond donors ≤ 5 0
  • H-bond acceptors ≤ 10 0
Veber's rules Pass
  • Rotatable bonds ≤ 10 0
  • TPSA ≤ 140 Ų 0.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1ccc2c(c1)CCC2
InChI 
InChI=1S/C9H10/c1-2-5-9-7-3-6-8(9)4-1/h1-2,4-5H,3,6-7H2
InChIKey 
PQNFLJBBNBOBRQ-UHFFFAOYSA-N

Provenance

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

Method
LigQ nearest_k
Source
PDB
Binding sites
PF00848

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_0611.

PDB 17

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

Ligand PDB entry

ZINC 50

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

Compound Similarity (Tanimoto)