Ligand profile

ZINC19789571

Virtual-screening candidate from ZINC.

Bound to: KP13_03495 — Histone deacetylase superfamily protein

Via homolog UniProt Q9Z2V5 Formula C₂₀H₂₅N₃O
Tanimoto 0.75
Mol. weight 323.44 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC19789571
UniProt (similar protein)
Q9Z2V5
Tanimoto
0.750
Target protein
KP13_03495

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 323.44 Da
LogP (Crippen) 2.36
H-bond donors 1
H-bond acceptors 3
TPSA 35.58 Ų
Rotatable bonds 5
Aromatic rings 2 / 3
Heavy atoms 24
Fraction sp³ C 0.35
Formula C₂₀H₂₅N₃O

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy High

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 35.6
  • −1 ≤ LogP ≤ 5 2.36
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 323.4
  • LogP ≤ 5 2.36
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 35.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CNC(=O)c1ccc(CN2CCN(Cc3ccccc3)CC2)cc1
InChI 
InChI=1S/C20H25N3O/c1-21-20(24)19-9-7-18(8-10-19)16-23-13-11-22(12-14-23)15-17-5-3-2-4-6-17/h2-10H,11-16H2,1H3,(H,21,24)
InChIKey 
WQTFPOVKDLNKNK-UHFFFAOYSA-N

Provenance

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

Method
LigQ nearest_k
Query
CHEMBL5192796
Homolog
Q9Z2V5

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_03495.

PDB 46

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

Ligand PDB entry

ChEMBL 55

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)