Ligand profile

3BY

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

Bound to: VK055_1464 — putative 2Fe-2S cluster-containing protein

Via homolog PDB 4qup UniProt Q92ZP9 Formula C₆H₁₁NO₂
Mol. weight 129.16 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
3BY
PDB
4qup
UniProt (similar protein)
Q92ZP9
Target protein
VK055_1464

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 129.16 Da
LogP (Crippen) 0.17
H-bond donors 1
H-bond acceptors 2
TPSA 40.54 Ų
Rotatable bonds 1
Aromatic rings 0 / 1
Heavy atoms 9
Fraction sp³ C 0.83
Formula C₆H₁₁NO₂

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 0.17
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 129.2
  • LogP ≤ 5 0.17
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 2
Veber's rules Pass
  • Rotatable bonds ≤ 10 1
  • TPSA ≤ 140 Ų 40.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CN1CCC[C@H]1C(=O)O
InChI 
InChI=1S/C6H11NO2/c1-7-4-2-3-5(7)6(8)9/h5H,2-4H2,1H3,(H,8,9)/t5-/m0/s1
InChIKey 
CWLQUGTUXBXTLF-YFKPBYRVSA-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
PF00848

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_1464.

PDB 7

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)