Ligand profile

VPU

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

Bound to: VK055_1361 — beta-hexosaminidase

Via homolog PDB 3gsm UniProt Q9KU37 Formula C₁₈H₂₅N₃O₇
Mol. weight 395.41 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
VPU
PDB
3gsm
UniProt (similar protein)
Q9KU37
Target protein
VK055_1361

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 395.41 Da
LogP (Crippen) 0.34
H-bond donors 5
H-bond acceptors 8
TPSA 149.71 Ų
Rotatable bonds 7
Aromatic rings 1 / 2
Heavy atoms 28
Fraction sp³ C 0.50
Formula C₁₈H₂₅N₃O₇

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 149.7
  • −1 ≤ LogP ≤ 5 0.34
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 395.4
  • LogP ≤ 5 0.34
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 8
Veber's rules Fail
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 149.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCCCC(=O)N[C@@H]\1[C@H]([C@@H]([C@H](O/C1=N\OC(=O)Nc2ccccc2)CO)O)O
InChI 
InChI=1S/C18H25N3O7/c1-2-3-9-13(23)20-14-16(25)15(24)12(10-22)27-17(14)21-28-18(26)19-11-7-5-4-6-8-11/h4-8,12,14-16,22,24-25H,2-3,9-10H2,1H3,(H,19,26)(H,20,23)/b21-17-/t12-,14-,15-,16-/m1/s1
InChIKey 
NUNQIQQEEPOGDJ-JDOAOKHLSA-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
PF00933

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_1361.

PDB 6

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ChEMBL 4

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)