Ligand profile

SEC

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

Bound to: VK055_0268 — yceI-like domain protein

Via homolog PDB 5w2v UniProt Q0PB90 Formula C₃H₇NO₂Se
Mol. weight 168.05 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
SEC
PDB
5w2v
UniProt (similar protein)
Q0PB90
Target protein
VK055_0268

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 168.05 Da
LogP (Crippen) -1.28
H-bond donors 2
H-bond acceptors 2
TPSA 63.32 Ų
Rotatable bonds 2
Aromatic rings 0 / 0
Heavy atoms 7
Fraction sp³ C 0.67
Formula C₃H₇NO₂Se

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 63.3
  • −1 ≤ LogP ≤ 5 -1.28
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 168.1
  • LogP ≤ 5 -1.28
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 2
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 63.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C([C@@H](C(=O)O)N)[SeH]
InChI 
InChI=1S/C3H7NO2Se/c4-2(1-7)3(5)6/h2,7H,1,4H2,(H,5,6)/t2-/m0/s1
InChIKey 
ZKZBPNGNEQAJSX-REOHCLBHSA-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
PF04264

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_0268.

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)