Ligand profile

1WN

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

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

Via homolog PDB 4lch UniProt P47205 Formula C₂₇H₂₃N₃O₅
Mol. weight 469.50 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
1WN
PDB
4lch
UniProt (similar protein)
P47205
Target protein
VK055_2471

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 469.50 Da
LogP (Crippen) 1.89
H-bond donors 6
H-bond acceptors 6
TPSA 144.91 Ų
Rotatable bonds 5
Aromatic rings 3 / 3
Heavy atoms 35
Fraction sp³ C 0.11
Formula C₂₇H₂₃N₃O₅

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 144.9
  • −1 ≤ LogP ≤ 5 1.89
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 469.5
  • LogP ≤ 5 1.89
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 6
Veber's rules Fail
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 144.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(c1ccc(cc1)O)(C(C(=O)NO)NC(=O)c2ccc(cc2)C#CC#Cc3ccc(cc3)N)O
InChI 
InChI=1S/C27H23N3O5/c1-27(34,21-12-16-23(31)17-13-21)24(26(33)30-35)29-25(32)20-10-6-18(7-11-20)4-2-3-5-19-8-14-22(28)15-9-19/h6-17,24,31,34-35H,28H2,1H3,(H,29,32)(H,30,33)
InChIKey 
CXPNZJDYPDDMKA-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)