Ligand profile

PBE

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

Bound to: VK055_4955 — substrate binding domain of ABC-type glycine betaine transport system family protein

Via homolog PDB 1sw1 UniProt O29280 Formula C₇H₁₄NO₂⁺
Mol. weight 144.19 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
PBE
PDB
1sw1
UniProt (similar protein)
O29280
Target protein
VK055_4955

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 144.19 Da
LogP (Crippen) 0.31
H-bond donors 1
H-bond acceptors 1
TPSA 37.30 Ų
Rotatable bonds 1
Aromatic rings 0 / 1
Heavy atoms 10
Fraction sp³ C 0.86
Formula C₇H₁₄NO₂⁺

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 37.3
  • −1 ≤ LogP ≤ 5 0.31
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 144.2
  • LogP ≤ 5 0.31
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 1
Veber's rules Pass
  • Rotatable bonds ≤ 10 1
  • TPSA ≤ 140 Ų 37.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[N+]1(CCC[C@H]1C(=O)O)C
InChI 
InChI=1S/C7H13NO2/c1-8(2)5-3-4-6(8)7(9)10/h6H,3-5H2,1-2H3/p+1/t6-/m0/s1
InChIKey 
CMUNUTVVOOHQPW-LURJTMIESA-O

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
PF04069

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_4955.

PDB 9

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

Ligand PDB entry

ZINC 26

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

Compound Similarity (Tanimoto)