Ligand profile

GBN

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

Bound to: VK055_3206 — branched-chain amino acid aminotransferase

Via homolog PDB 2ej3 UniProt Q5SM19 Formula C₉H₁₇NO₂
Mol. weight 171.24 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
GBN
PDB
2ej3
UniProt (similar protein)
Q5SM19
Target protein
VK055_3206

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 171.24 Da
LogP (Crippen) 1.37
H-bond donors 2
H-bond acceptors 2
TPSA 63.32 Ų
Rotatable bonds 3
Aromatic rings 0 / 1
Heavy atoms 12
Fraction sp³ C 0.89
Formula C₉H₁₇NO₂

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 1.37
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 171.2
  • LogP ≤ 5 1.37
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 2
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 63.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C1CCC(CC1)(CC(=O)O)CN
InChI 
InChI=1S/C9H17NO2/c10-7-9(6-8(11)12)4-2-1-3-5-9/h1-7,10H2,(H,11,12)
InChIKey 
UGJMXCAKCUNAIE-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
PF01063

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_3206.

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)