Ligand profile

3P3

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

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

Via homolog PDB 3p3e UniProt P47205 Formula C₂₁H₁₈N₂O₄
Mol. weight 362.39 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
3P3
PDB
3p3e
UniProt (similar protein)
P47205
Target protein
VK055_2471

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 362.39 Da
LogP (Crippen) 1.07
H-bond donors 4
H-bond acceptors 4
TPSA 98.66 Ų
Rotatable bonds 4
Aromatic rings 2 / 2
Heavy atoms 27
Fraction sp³ C 0.14
Formula C₂₁H₁₈N₂O₄

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 98.7
  • −1 ≤ LogP ≤ 5 1.07
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 362.4
  • LogP ≤ 5 1.07
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 98.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(C(C(=O)NO)NC(=O)c1ccc(cc1)C#CC#Cc2ccccc2)O
InChI 
InChI=1S/C21H18N2O4/c1-15(24)19(21(26)23-27)22-20(25)18-13-11-17(12-14-18)10-6-5-9-16-7-3-2-4-8-16/h2-4,7-8,11-15,19,24,27H,1H3,(H,22,25)(H,23,26)
InChIKey 
VUYMSCCEGRLBAF-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)