Ligand profile

JWM

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

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

Via homolog PDB 6mo4 UniProt P47205 Formula C₁₉H₂₂N₂O₆S
Mol. weight 406.46 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
JWM
PDB
6mo4
UniProt (similar protein)
P47205
Target protein
VK055_2471

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 406.46 Da
LogP (Crippen) -0.15
H-bond donors 4
H-bond acceptors 6
TPSA 132.80 Ų
Rotatable bonds 6
Aromatic rings 1 / 1
Heavy atoms 28
Fraction sp³ C 0.37
Formula C₁₉H₂₂N₂O₆S

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 132.8
  • −1 ≤ LogP ≤ 5 -0.15
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 406.5
  • LogP ≤ 5 -0.15
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 132.8
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#CCCO)S(=O)(=O)C
InChI 
InChI=1S/C19H22N2O6S/c1-19(2,28(3,26)27)16(18(24)21-25)20-17(23)15-11-9-14(10-12-15)8-6-4-5-7-13-22/h9-12,16,22,25H,7,13H2,1-3H3,(H,20,23)(H,21,24)
InChIKey 
RFKFCSZMHYSIDP-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)