Ligand profile

D3M

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

Bound to: VK055_0826 — rieske [2Fe-2S] domain protein

Via homolog PDB 3gb4 UniProt Q5S3I3 Formula C₈H₆Cl₂O₃
Mol. weight 221.04 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
D3M
PDB
3gb4
UniProt (similar protein)
Q5S3I3
Target protein
VK055_0826

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 221.04 Da
LogP (Crippen) 2.70
H-bond donors 1
H-bond acceptors 2
TPSA 46.53 Ų
Rotatable bonds 2
Aromatic rings 1 / 1
Heavy atoms 13
Fraction sp³ C 0.12
Formula C₈H₆Cl₂O₃

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 46.5
  • −1 ≤ LogP ≤ 5 2.70
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 221.0
  • LogP ≤ 5 2.70
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 2
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 46.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
COc1c(ccc(c1C(=O)O)Cl)Cl
InChI 
InChI=1S/C8H6Cl2O3/c1-13-7-5(10)3-2-4(9)6(7)8(11)12/h2-3H,1H3,(H,11,12)
InChIKey 
IWEDIXLBFLAXBO-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
PF19112

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_0826.

PDB 7

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)