Ligand profile

V87

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

Bound to: VK055_3681 — rhomboid family protease GlpG

Via homolog PDB 6xrp UniProt P09391 Formula C₁₁H₁₅NO
Mol. weight 177.25 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
V87
PDB
6xrp
UniProt (similar protein)
P09391
Target protein
VK055_3681

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 177.25 Da
LogP (Crippen) 1.76
H-bond donors 1
H-bond acceptors 1
TPSA 29.10 Ų
Rotatable bonds 6
Aromatic rings 1 / 1
Heavy atoms 13
Fraction sp³ C 0.36
Formula C₁₁H₁₅NO

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 29.1
  • −1 ≤ LogP ≤ 5 1.76
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 177.2
  • LogP ≤ 5 1.76
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 1
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 29.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1ccc(cc1)CCCCNC=O
InChI 
InChI=1S/C11H15NO/c13-10-12-9-5-4-8-11-6-2-1-3-7-11/h1-3,6-7,10H,4-5,8-9H2,(H,12,13)
InChIKey 
FSDTVSVBONVQBJ-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
PF01694

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_3681.

PDB 8

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)