Ligand profile

GBL

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

Bound to: VK055_0721 — putative gamma-glutamyltransferase ywrD

Via homolog PDB 7d9x UniProt A0A6G6IRK3 Formula C₄H₆O₂
Mol. weight 86.09 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
GBL
PDB
7d9x
UniProt (similar protein)
A0A6G6IRK3
Target protein
VK055_0721

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 86.09 Da
LogP (Crippen) 0.32
H-bond donors 0
H-bond acceptors 2
TPSA 26.30 Ų
Rotatable bonds 0
Aromatic rings 0 / 1
Heavy atoms 6
Fraction sp³ C 0.75
Formula C₄H₆O₂

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 26.3
  • −1 ≤ LogP ≤ 5 0.32
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 86.1
  • LogP ≤ 5 0.32
  • H-bond donors ≤ 5 0
  • H-bond acceptors ≤ 10 2
Veber's rules Pass
  • Rotatable bonds ≤ 10 0
  • TPSA ≤ 140 Ų 26.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C1CC(=O)OC1
InChI 
InChI=1S/C4H6O2/c5-4-2-1-3-6-4/h1-3H2
InChIKey 
YEJRWHAVMIAJKC-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
PF01019

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_0721.

PDB 7

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)