Ligand profile

FYL

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

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

Via homolog PDB 7ci9 UniProt P47205 Formula C₂₁H₂₄N₄O₅
Mol. weight 412.45 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
FYL
PDB
7ci9
UniProt (similar protein)
P47205
Target protein
VK055_2471

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 412.45 Da
LogP (Crippen) 0.43
H-bond donors 4
H-bond acceptors 9
TPSA 139.79 Ų
Rotatable bonds 8
Aromatic rings 3 / 3
Heavy atoms 30
Fraction sp³ C 0.33
Formula C₂₁H₂₄N₄O₅

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 139.8
  • −1 ≤ LogP ≤ 5 0.43
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 412.4
  • LogP ≤ 5 0.43
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 9
Veber's rules Pass
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 139.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(c1nccn1Cc2cc(on2)C#Cc3ccc(cc3)OCC(CO)(CO)N)O
InChI 
InChI=1S/C21H24N4O5/c1-15(28)20-23-8-9-25(20)11-17-10-19(30-24-17)7-4-16-2-5-18(6-3-16)29-14-21(22,12-26)13-27/h2-3,5-6,8-10,15,26-28H,11-14,22H2,1H3
InChIKey 
DKGUWMFQYQOPSO-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)