Ligand profile

1WM

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

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

Via homolog PDB 4lcg UniProt P47205 Formula C₂₆H₂₁N₃O₅
Mol. weight 455.47 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
1WM
PDB
4lcg
UniProt (similar protein)
P47205
Target protein
VK055_2471

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 455.47 Da
LogP (Crippen) 1.71
H-bond donors 6
H-bond acceptors 6
TPSA 144.91 Ų
Rotatable bonds 5
Aromatic rings 3 / 3
Heavy atoms 34
Fraction sp³ C 0.08
Formula C₂₆H₂₁N₃O₅

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 1.71
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 455.5
  • LogP ≤ 5 1.71
  • 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 
c1cc(ccc1C#CC#Cc2ccc(cc2)N)C(=O)NC(C(c3ccc(cc3)O)O)C(=O)NO
InChI 
InChI=1S/C26H21N3O5/c27-21-13-7-18(8-14-21)4-2-1-3-17-5-9-20(10-6-17)25(32)28-23(26(33)29-34)24(31)19-11-15-22(30)16-12-19/h5-16,23-24,30-31,34H,27H2,(H,28,32)(H,29,33)
InChIKey 
WYPQPFTULGRIPE-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)