Ligand profile

ZINC5439364

Virtual-screening candidate from ZINC.

Bound to: KP13_31490 — Beta-hexosaminidase

Via homolog UniProt Q5FA94 Formula C₉H₁₈N₂O₆
Tanimoto 0.57
Mol. weight 250.25 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC5439364
UniProt (similar protein)
Q5FA94
Tanimoto
0.575
Target protein
KP13_31490

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 250.25 Da
LogP (Crippen) -3.75
H-bond donors 6
H-bond acceptors 7
TPSA 145.27 Ų
Rotatable bonds 3
Aromatic rings 0 / 1
Heavy atoms 17
Fraction sp³ C 0.89
Formula C₉H₁₈N₂O₆

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 145.3
  • −1 ≤ LogP ≤ 5 -3.75
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 250.3
  • LogP ≤ 5 -3.75
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 7
Veber's rules Fail
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 145.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@H](N)C(=O)N[C@@H]1[C@@H](O)O[C@@H](CO)[C@@H](O)[C@H]1O
InChI 
InChI=1S/C9H18N2O6/c1-3(10)8(15)11-5-7(14)6(13)4(2-12)17-9(5)16/h3-7,9,12-14,16H,2,10H2,1H3,(H,11,15)/t3-,4-,5-,6+,7-,9-/m0/s1
InChIKey 
HKCPYXFUQPLJOF-ZDMURPDRSA-N

Provenance

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

Method
LigQ nearest_k
Query
C76
Homolog
Q5FA94

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to KP13_31490.

PDB 7

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 49

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

Compound Similarity (Tanimoto)