Ligand profile

NOK

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

Bound to: VK055_1361 — beta-hexosaminidase

Via homolog PDB 5g5k UniProt Q9HZK0 Formula C₈H₁₆N₂O₄
Mol. weight 204.23 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
NOK
PDB
5g5k
UniProt (similar protein)
Q9HZK0
Target protein
VK055_1361

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 204.23 Da
LogP (Crippen) -2.82
H-bond donors 5
H-bond acceptors 5
TPSA 101.82 Ų
Rotatable bonds 2
Aromatic rings 0 / 1
Heavy atoms 14
Fraction sp³ C 0.88
Formula C₈H₁₆N₂O₄

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 101.8
  • −1 ≤ LogP ≤ 5 -2.82
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 204.2
  • LogP ≤ 5 -2.82
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 101.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(=O)N[C@H]1CN[C@@H]([C@H]([C@@H]1O)O)CO
InChI 
InChI=1S/C8H16N2O4/c1-4(12)10-5-2-9-6(3-11)8(14)7(5)13/h5-9,11,13-14H,2-3H2,1H3,(H,10,12)/t5-,6+,7+,8+/m0/s1
InChIKey 
GBRAQQUMMCVTAV-LXGUWJNJSA-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)