Ligand profile

GOI

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

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

Via homolog PDB 3vip UniProt Q8T0W7 Formula C₂₉H₃₉N₃O₆
Mol. weight 525.65 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
GOI
PDB
3vip
UniProt (similar protein)
Q8T0W7
Target protein
VK055_4152

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 525.65 Da
LogP (Crippen) 1.13
H-bond donors 4
H-bond acceptors 9
TPSA 109.10 Ų
Rotatable bonds 9
Aromatic rings 2 / 5
Heavy atoms 38
Fraction sp³ C 0.52
Formula C₂₉H₃₉N₃O₆

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 109.1
  • −1 ≤ LogP ≤ 5 1.13
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 525.6
  • LogP ≤ 5 1.13
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 9
Veber's rules Pass
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 109.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1ccc2c(c1)C=Cc3ccccc3N2CCCN4CCN(CC4)CCO[C@H]5[C@@H]([C@H]([C@@H]([C@H](O5)CO)O)O)O
InChI 
InChI=1S/C29H39N3O6/c33-20-25-26(34)27(35)28(36)29(38-25)37-19-18-31-16-14-30(15-17-31)12-5-13-32-23-8-3-1-6-21(23)10-11-22-7-2-4-9-24(22)32/h1-4,6-11,25-29,33-36H,5,12-20H2/t25-,26-,27+,28-,29-/m1/s1
InChIKey 
GVUGRCGKZRTSLY-XYPQWYOHSA-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)