Ligand profile

BSY

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

Bound to: VK055_0238 — nitrate reductase, alpha subunit

Via homolog PDB 5chc UniProt G8QM55 Formula HO₃Se⁻
Mol. weight 127.96 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
BSY
PDB
5chc
UniProt (similar protein)
G8QM55
Target protein
VK055_0238

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 127.96 Da
LogP (Crippen) -2.25
H-bond donors 1
H-bond acceptors 2
TPSA 60.36 Ų
Rotatable bonds 0
Aromatic rings 0 / 0
Heavy atoms 4
Fraction sp³ C 0.00
Formula HO₃Se⁻

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 60.4
  • −1 ≤ LogP ≤ 5 -2.25
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 128.0
  • LogP ≤ 5 -2.25
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 2
Veber's rules Pass
  • Rotatable bonds ≤ 10 0
  • TPSA ≤ 140 Ų 60.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
O[Se](=O)[O-]
InChI 
InChI=1S/H2O3Se/c1-4(2)3/h(H2,1,2,3)/p-1
InChIKey 
MCAHWIHFGHIESP-UHFFFAOYSA-M

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
PF00384

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_0238.

PDB 12

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)