Ligand profile

MSF

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

Bound to: VK055_2309 — L-2-hydroxyglutarate oxidase

Via homolog PDB 1el8 UniProt P40859 Formula C₃H₅O₂Se⁻
Mol. weight 152.03 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
MSF
PDB
1el8
UniProt (similar protein)
P40859
Target protein
VK055_2309

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 152.03 Da
LogP (Crippen) -1.09
H-bond donors 0
H-bond acceptors 2
TPSA 40.13 Ų
Rotatable bonds 2
Aromatic rings 0 / 0
Heavy atoms 6
Fraction sp³ C 0.67
Formula C₃H₅O₂Se⁻

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 40.1
  • −1 ≤ LogP ≤ 5 -1.09
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 152.0
  • LogP ≤ 5 -1.09
  • H-bond donors ≤ 5 0
  • H-bond acceptors ≤ 10 2
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 40.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[Se]CC(=O)[O-]
InChI 
InChI=1S/C3H6O2Se/c1-6-2-3(4)5/h2H2,1H3,(H,4,5)/p-1
InChIKey 
UOULLTHLSZQUIN-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
PF01266

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_2309.

PDB 10

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)