Ligand profile

5EN

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

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

Via homolog PDB 5drr UniProt P47205 Formula C₂₂H₁₉F₂N₃O₄
Mol. weight 427.41 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
5EN
PDB
5drr
UniProt (similar protein)
P47205
Target protein
VK055_2471

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 427.41 Da
LogP (Crippen) 1.29
H-bond donors 5
H-bond acceptors 5
TPSA 124.68 Ų
Rotatable bonds 5
Aromatic rings 2 / 2
Heavy atoms 31
Fraction sp³ C 0.18
Formula C₂₂H₁₉F₂N₃O₄

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 124.7
  • −1 ≤ LogP ≤ 5 1.29
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 427.4
  • LogP ≤ 5 1.29
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 124.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(C(C(=O)NO)NC(=O)c1ccc(cc1)C#CC#Cc2ccc(cc2)N)(C(F)F)O
InChI 
InChI=1S/C22H19F2N3O4/c1-22(30,21(23)24)18(20(29)27-31)26-19(28)16-10-6-14(7-11-16)4-2-3-5-15-8-12-17(25)13-9-15/h6-13,18,21,30-31H,25H2,1H3,(H,26,28)(H,27,29)
InChIKey 
HJOKUNVOXGDMLS-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)