Ligand profile

LSY

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

Bound to: VK055_4524 — transcription activator HlyU

Via homolog PDB 6o8m UniProt D5AT91 Formula C₆H₁₄N₄O₂
Mol. weight 174.20 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
LSY
PDB
6o8m
UniProt (similar protein)
D5AT91
Target protein
VK055_4524

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 174.20 Da
LogP (Crippen) -0.56
H-bond donors 2
H-bond acceptors 2
TPSA 64.68 Ų
Rotatable bonds 0
Aromatic rings 0 / 0
Heavy atoms 12
Fraction sp³ C 0.67
Formula C₆H₁₄N₄O₂

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 64.7
  • −1 ≤ LogP ≤ 5 -0.56
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 174.2
  • LogP ≤ 5 -0.56
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 2
Veber's rules Pass
  • Rotatable bonds ≤ 10 0
  • TPSA ≤ 140 Ų 64.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CN(C)C(=O)NNC(=O)N(C)C
InChI 
InChI=1S/C6H14N4O2/c1-9(2)5(11)7-8-6(12)10(3)4/h1-4H3,(H,7,11)(H,8,12)
InChIKey 
RAUKYARZDOSMOO-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
PF01022

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_4524.

ZINC 3

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

Compound Similarity (Tanimoto)