Ligand profile

SYN

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

Bound to: VK055_3138 — 3-octaprenyl-4-hydroxybenzoate decarboxylase

Via homolog PDB 6r3l UniProt A2QHE5 Formula C₈H₈
Mol. weight 104.15 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
SYN
PDB
6r3l
UniProt (similar protein)
A2QHE5
Target protein
VK055_3138

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 104.15 Da
LogP (Crippen) 2.33
H-bond donors 0
H-bond acceptors 0
TPSA 0.00 Ų
Rotatable bonds 1
Aromatic rings 1 / 1
Heavy atoms 8
Fraction sp³ C 0.00
Formula C₈H₈

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 2.33
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 104.2
  • LogP ≤ 5 2.33
  • H-bond donors ≤ 5 0
  • H-bond acceptors ≤ 10 0
Veber's rules Pass
  • Rotatable bonds ≤ 10 1
  • TPSA ≤ 140 Ų 0.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C=Cc1ccccc1
InChI 
InChI=1S/C8H8/c1-2-8-6-4-3-5-7-8/h2-7H,1H2
InChIKey 
PPBRXRYQALVLMV-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
PF01977' 'PF20696

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_3138.

PDB 21

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)