Ligand profile

H9J

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

Bound to: VK055_1361 — beta-hexosaminidase

Via homolog PDB 6dte UniProt A0A125HFC0 Formula C₉H₁₄F₃NO₆
Mol. weight 289.21 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
H9J
PDB
6dte
UniProt (similar protein)
A0A125HFC0
Target protein
VK055_1361

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 289.21 Da
LogP (Crippen) -2.90
H-bond donors 6
H-bond acceptors 6
TPSA 130.25 Ų
Rotatable bonds 2
Aromatic rings 0 / 1
Heavy atoms 19
Fraction sp³ C 0.89
Formula C₉H₁₄F₃NO₆

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 130.2
  • −1 ≤ LogP ≤ 5 -2.90
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 289.2
  • LogP ≤ 5 -2.90
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 130.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C(C1[C@H]([C@@H](C([C@H]([C@@H]1O)O)NC(=O)C(F)(F)F)O)O)O
InChI 
InChI=1S/C9H14F3NO6/c10-9(11,12)8(19)13-3-6(17)4(15)2(1-14)5(16)7(3)18/h2-7,14-18H,1H2,(H,13,19)/t2?,3?,4-,5-,6-,7-/m1/s1
InChIKey 
RPAYCNWWSJECNN-WMBSXCRSSA-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)