Ligand profile

GBE

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

Bound to: VK055_4152 — aryl-phospho-beta-D-glucosidase BglA

Via homolog PDB 3vio UniProt Q8T0W7 Formula C₁₅H₃₀N₂O₉S
Mol. weight 414.48 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
GBE
PDB
3vio
UniProt (similar protein)
Q8T0W7
Target protein
VK055_4152

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 414.48 Da
LogP (Crippen) -3.30
H-bond donors 5
H-bond acceptors 10
TPSA 160.23 Ų
Rotatable bonds 9
Aromatic rings 0 / 2
Heavy atoms 27
Fraction sp³ C 1.00
Formula C₁₅H₃₀N₂O₉S

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 160.2
  • −1 ≤ LogP ≤ 5 -3.30
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 414.5
  • LogP ≤ 5 -3.30
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 10
Veber's rules Fail
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 160.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C1CN(CCN1CCCS(=O)(=O)O)CCO[C@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CO)O)O)O
InChI 
InChI=1S/C15H30N2O9S/c18-10-11-12(19)13(20)14(21)15(26-11)25-8-7-17-5-3-16(4-6-17)2-1-9-27(22,23)24/h11-15,18-21H,1-10H2,(H,22,23,24)/t11-,12-,13+,14-,15-/m1/s1
InChIKey 
DAJNLGJHGLHERP-UXXRCYHCSA-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
PF00232

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_4152.

PDB 11

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ZINC 15

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)