Ligand profile

5EM

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

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

Via homolog PDB 5drq UniProt P47205 Formula C₂₂H₂₂N₄O₃
Mol. weight 390.44 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
5EM
PDB
5drq
UniProt (similar protein)
P47205
Target protein
VK055_2471

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 390.44 Da
LogP (Crippen) 1.01
H-bond donors 5
H-bond acceptors 5
TPSA 130.47 Ų
Rotatable bonds 4
Aromatic rings 2 / 2
Heavy atoms 29
Fraction sp³ C 0.18
Formula C₂₂H₂₂N₄O₃

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 130.5
  • −1 ≤ LogP ≤ 5 1.01
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 390.4
  • LogP ≤ 5 1.01
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 130.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(C)(C(C(=O)NO)NC(=O)c1ccc(cc1)C#CC#Cc2ccc(cc2)N)N
InChI 
InChI=1S/C22H22N4O3/c1-22(2,24)19(21(28)26-29)25-20(27)17-11-7-15(8-12-17)5-3-4-6-16-9-13-18(23)14-10-16/h7-14,19,29H,23-24H2,1-2H3,(H,25,27)(H,26,28)
InChIKey 
VVHQDGBAFRDCKP-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)