Ligand profile

XBZ

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

Bound to: VK055_3858 — aerobic respiration control sensor protein arcB

Via homolog PDB 5hww UniProt A5W4E3 Formula C₉H₁₂
Mol. weight 120.19 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
XBZ
PDB
5hww
UniProt (similar protein)
A5W4E3
Target protein
VK055_3858

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 120.19 Da
LogP (Crippen) 2.61
H-bond donors 0
H-bond acceptors 0
TPSA 0.00 Ų
Rotatable bonds 0
Aromatic rings 1 / 1
Heavy atoms 9
Fraction sp³ C 0.33
Formula C₉H₁₂

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 2.61
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 120.2
  • LogP ≤ 5 2.61
  • H-bond donors ≤ 5 0
  • H-bond acceptors ≤ 10 0
Veber's rules Pass
  • Rotatable bonds ≤ 10 0
  • TPSA ≤ 140 Ų 0.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1ccc(c(c1)C)C
InChI 
InChI=1S/C9H12/c1-7-4-5-8(2)9(3)6-7/h4-6H,1-3H3
InChIKey 
GWHJZXXIDMPWGX-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
PF08448

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_3858.

PDB 4

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)