Ligand profile

L52

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

Bound to: VK055_2471 — UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosaminedeacetylase

Via homolog PDB 4fw3 UniProt P47205 Formula C₂₀H₁₇N₃O₃
Mol. weight 347.37 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
L52
PDB
4fw3
UniProt (similar protein)
P47205
Target protein
VK055_2471

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 347.37 Da
LogP (Crippen) 0.65
H-bond donors 4
H-bond acceptors 4
TPSA 104.45 Ų
Rotatable bonds 4
Aromatic rings 2 / 2
Heavy atoms 26
Fraction sp³ C 0.10
Formula C₂₀H₁₇N₃O₃

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy Check

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 104.5
  • −1 ≤ LogP ≤ 5 0.65
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 347.4
  • LogP ≤ 5 0.65
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 104.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1ccc(cc1)C#CC#Cc2ccc(cc2)C(=O)NC(CN)C(=O)NO
InChI 
InChI=1S/C20H17N3O3/c21-14-18(20(25)23-26)22-19(24)17-12-10-16(11-13-17)9-5-4-8-15-6-2-1-3-7-15/h1-3,6-7,10-13,18,26H,14,21H2,(H,22,24)(H,23,25)
InChIKey 
RMTUQHBOIGEBSC-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
PF03331

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_2471.

PDB 40

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

Ligand PDB entry

ChEMBL 100

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 50

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

Compound Similarity (Tanimoto)