Ligand profile

AE3

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

Bound to: VK055_0661 — bacterial alpha-L-rhamnosidase family protein

Via homolog PDB 6i60 UniProt B5YC64 Formula C₆H₁₄O₃
Mol. weight 134.18 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
AE3
PDB
6i60
UniProt (similar protein)
B5YC64
Target protein
VK055_0661

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 134.18 Da
LogP (Crippen) 0.03
H-bond donors 1
H-bond acceptors 3
TPSA 38.69 Ų
Rotatable bonds 6
Aromatic rings 0 / 0
Heavy atoms 9
Fraction sp³ C 1.00
Formula C₆H₁₄O₃

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 38.7
  • −1 ≤ LogP ≤ 5 0.03
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 134.2
  • LogP ≤ 5 0.03
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 38.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCOCCOCCO
InChI 
InChI=1S/C6H14O3/c1-2-8-5-6-9-4-3-7/h7H,2-6H2,1H3
InChIKey 
XXJWXESWEXIICW-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
PF05592' 'PF08531' 'PF17389

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_0661.

ZINC 50

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

Compound Similarity (Tanimoto)