Ligand profile

ZINC584906746

Virtual-screening candidate from ZINC.

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

Via homolog UniProt P0A725 Formula C₂₀H₂₀N₂O₄
Tanimoto 0.67
Mol. weight 352.39 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC584906746
UniProt (similar protein)
P0A725
Tanimoto
0.674
Target protein
VK055_2471

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 352.39 Da
LogP (Crippen) 1.32
H-bond donors 3
H-bond acceptors 5
TPSA 101.65 Ų
Rotatable bonds 4
Aromatic rings 2 / 2
Heavy atoms 26
Fraction sp³ C 0.20
Formula C₂₀H₂₀N₂O₄

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 101.7
  • −1 ≤ LogP ≤ 5 1.32
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 352.4
  • LogP ≤ 5 1.32
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 101.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
COC(=O)[C@@H](NC(=O)c1ccc(C#Cc2ccc(N)cc2)cc1)[C@@H](C)O
InChI 
InChI=1S/C20H20N2O4/c1-13(23)18(20(25)26-2)22-19(24)16-9-5-14(6-10-16)3-4-15-7-11-17(21)12-8-15/h5-13,18,23H,21H2,1-2H3,(H,22,24)/t13-,18+/m1/s1
InChIKey 
TYANENYPQMSXEY-ACJLOTCBSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ sequence
Query
CHEMBL1643369
Homolog
P0A725

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 41

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 49

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)