Ligand profile

GST

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

Bound to: VK055_3045 — 4-hydroxybenzoate polyprenyl transferase

Via homolog PDB 4od5 UniProt Q9YBM8 Formula C₁₀H₂₀O₆P₂S
Mol. weight 330.28 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
GST
PDB
4od5
UniProt (similar protein)
Q9YBM8
Target protein
VK055_3045

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 330.28 Da
LogP (Crippen) 3.62
H-bond donors 3
H-bond acceptors 4
TPSA 104.06 Ų
Rotatable bonds 8
Aromatic rings 0 / 0
Heavy atoms 19
Fraction sp³ C 0.60
Formula C₁₀H₂₀O₆P₂S

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 104.1
  • −1 ≤ LogP ≤ 5 3.62
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 330.3
  • LogP ≤ 5 3.62
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 104.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(=CCCC(=CCS[P@](=O)(O)OP(=O)(O)O)C)C
InChI 
InChI=1S/C10H20O6P2S/c1-9(2)5-4-6-10(3)7-8-19-18(14,15)16-17(11,12)13/h5,7H,4,6,8H2,1-3H3,(H,14,15)(H2,11,12,13)
InChIKey 
AKIXWSDUEPPMKM-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
PF01040

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_3045.

PDB 1

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)