Ligand profile

SEY

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

Bound to: KP13_02811 — Glycerol-3-phosphate acyltransferase

Via homolog PDB 7cqm UniProt O66905 Formula CH₄N₂Se
Mol. weight 123.02 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
SEY
PDB
7cqm
UniProt (similar protein)
O66905
Target protein
KP13_02811

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 123.02 Da
LogP (Crippen) -1.84
H-bond donors 2
H-bond acceptors 2
TPSA 52.04 Ų
Rotatable bonds 0
Aromatic rings 0 / 0
Heavy atoms 4
Fraction sp³ C 0.00
Formula CH₄N₂Se

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 52.0
  • −1 ≤ LogP ≤ 5 -1.84
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 123.0
  • LogP ≤ 5 -1.84
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 2
Veber's rules Pass
  • Rotatable bonds ≤ 10 0
  • TPSA ≤ 140 Ų 52.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C(=[Se])(N)N
InChI 
InChI=1S/CH4N2Se/c2-1(3)4/h(H4,2,3,4)
InChIKey 
IYKVLICPFCEZOF-UHFFFAOYSA-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
PF02660

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to KP13_02811.

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)