Ligand profile

1WL

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

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

Via homolog PDB 4lcf UniProt P47205 Formula C₂₃H₁₉N₅O₃
Mol. weight 413.44 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
1WL
PDB
4lcf
UniProt (similar protein)
P47205
Target protein
VK055_2471

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 413.44 Da
LogP (Crippen) 1.24
H-bond donors 5
H-bond acceptors 5
TPSA 133.13 Ų
Rotatable bonds 5
Aromatic rings 3 / 3
Heavy atoms 31
Fraction sp³ C 0.09
Formula C₂₃H₁₉N₅O₃

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 133.1
  • −1 ≤ LogP ≤ 5 1.24
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 413.4
  • LogP ≤ 5 1.24
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 133.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc(ccc1C#CC#Cc2ccc(cc2)N)C(=O)NC(Cc3cnc[nH]3)C(=O)NO
InChI 
InChI=1S/C23H19N5O3/c24-19-11-7-17(8-12-19)4-2-1-3-16-5-9-18(10-6-16)22(29)27-21(23(30)28-31)13-20-14-25-15-26-20/h5-12,14-15,21,31H,13,24H2,(H,25,26)(H,27,29)(H,28,30)
InChIKey 
AEXNUUIGAXOZGM-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)