Ligand profile

MSE

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

Bound to: KP13_00014 — Regulatory protein asnC

Via homolog PDB 2e1a UniProt O73983 Formula C₅H₁₁NO₂Se
Mol. weight 196.11 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
MSE
PDB
2e1a
UniProt (similar protein)
O73983
Target protein
KP13_00014

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 196.11 Da
LogP (Crippen) -0.04
H-bond donors 2
H-bond acceptors 2
TPSA 63.32 Ų
Rotatable bonds 4
Aromatic rings 0 / 0
Heavy atoms 9
Fraction sp³ C 0.80
Formula C₅H₁₁NO₂Se

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 63.3
  • −1 ≤ LogP ≤ 5 -0.04
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 196.1
  • LogP ≤ 5 -0.04
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 2
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 63.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[Se]CC[C@@H](C(=O)O)N
InChI 
InChI=1S/C5H11NO2Se/c1-9-3-2-4(6)5(7)8/h4H,2-3,6H2,1H3,(H,7,8)/t4-/m0/s1
InChIKey 
RJFAYQIBOAGBLC-BYPYZUCNSA-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
PF01037

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_00014.

ZINC 50

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

Compound Similarity (Tanimoto)