Ligand profile

IDM

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

Bound to: VK055_1196 — tryptophan synthase, beta subunit

Via homolog PDB 3cep UniProt P0A2K1 Formula C₈H₉N
Mol. weight 119.17 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
IDM
PDB
3cep
UniProt (similar protein)
P0A2K1
Target protein
VK055_1196

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 119.17 Da
LogP (Crippen) 1.65
H-bond donors 1
H-bond acceptors 1
TPSA 12.03 Ų
Rotatable bonds 0
Aromatic rings 1 / 2
Heavy atoms 9
Fraction sp³ C 0.25
Formula C₈H₉N

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 12.0
  • −1 ≤ LogP ≤ 5 1.65
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 119.2
  • LogP ≤ 5 1.65
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 1
Veber's rules Pass
  • Rotatable bonds ≤ 10 0
  • TPSA ≤ 140 Ų 12.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1ccc2c(c1)CCN2
InChI 
InChI=1S/C8H9N/c1-2-4-8-7(3-1)5-6-9-8/h1-4,9H,5-6H2
InChIKey 
LPAGFVYQRIESJQ-UHFFFAOYSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ sequence
Source
PDB
Binding sites
PF00290' 'PF00291

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_1196.

PDB 40

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)