Ligand profile

9JE

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

Bound to: VK055_4419 — phenolic acid decarboxylase subunit C

Via homolog PDB 5o3m UniProt A6T7M3 Formula C₅H₁₂O₂
Mol. weight 104.15 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
9JE
PDB
5o3m
UniProt (similar protein)
A6T7M3
Target protein
VK055_4419

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 104.15 Da
LogP (Crippen) 0.14
H-bond donors 2
H-bond acceptors 2
TPSA 40.46 Ų
Rotatable bonds 4
Aromatic rings 0 / 0
Heavy atoms 7
Fraction sp³ C 1.00
Formula C₅H₁₂O₂

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 40.5
  • −1 ≤ LogP ≤ 5 0.14
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 104.1
  • LogP ≤ 5 0.14
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 2
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 40.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C(CCO)CCO
InChI 
InChI=1S/C5H12O2/c6-4-2-1-3-5-7/h6-7H,1-5H2
InChIKey 
ALQSHHUCVQOPAS-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
PF01977' 'PF20696

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_4419.

PDB 2

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ZINC 37

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

Compound Similarity (Tanimoto)