Ligand profile

SEK

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

Bound to: VK055_3475 — voltage gated chloride channel family protein

Via homolog PDB 2h2p UniProt P37019 Formula CNSe⁻
Mol. weight 104.98 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
SEK
PDB
2h2p
UniProt (similar protein)
P37019
Target protein
VK055_3475

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 104.98 Da
LogP (Crippen) -0.36
H-bond donors 0
H-bond acceptors 1
TPSA 23.79 Ų
Rotatable bonds 0
Aromatic rings 0 / 0
Heavy atoms 3
Fraction sp³ C 0.00
Formula CNSe⁻

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 23.8
  • −1 ≤ LogP ≤ 5 -0.36
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 105.0
  • LogP ≤ 5 -0.36
  • H-bond donors ≤ 5 0
  • H-bond acceptors ≤ 10 1
Veber's rules Pass
  • Rotatable bonds ≤ 10 0
  • TPSA ≤ 140 Ų 23.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C(#N)[Se-]
InChI 
InChI=1S/CHNSe/c2-1-3/h3H/p-1
InChIKey 
CRDYSYOERSZTHZ-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
PF00654

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_3475.

PDB 2

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

Ligand PDB entry

ZINC 46

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

Compound Similarity (Tanimoto)