Ligand profile

PG5

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

Bound to: VK055_3519 — serine O-acetyltransferase

Via homolog PDB 3gvd UniProt A0A2U2H3H7 Formula C₈H₁₈O₄
Mol. weight 178.23 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
PG5
PDB
3gvd
UniProt (similar protein)
A0A2U2H3H7
Target protein
VK055_3519

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 178.23 Da
LogP (Crippen) 0.31
H-bond donors 0
H-bond acceptors 4
TPSA 36.92 Ų
Rotatable bonds 9
Aromatic rings 0 / 0
Heavy atoms 12
Fraction sp³ C 1.00
Formula C₈H₁₈O₄

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 36.9
  • −1 ≤ LogP ≤ 5 0.31
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 178.2
  • LogP ≤ 5 0.31
  • H-bond donors ≤ 5 0
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 36.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
COCCOCCOCCOC
InChI 
InChI=1S/C8H18O4/c1-9-3-5-11-7-8-12-6-4-10-2/h3-8H2,1-2H3
InChIKey 
YFNKIDBQEZZDLK-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
PF06426

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_3519.

PDB 2

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)