Ligand profile

ZINC84596120

Virtual-screening candidate from ZINC.

Bound to: KP13_03495 — Histone deacetylase superfamily protein

Via homolog UniProt Q9Z2V5 Formula C₂₀H₂₁N₃O₂
Tanimoto 0.84
Mol. weight 335.41 Da
Permeability High
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC84596120
UniProt (similar protein)
Q9Z2V5
Tanimoto
0.840
Target protein
KP13_03495

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 335.41 Da
LogP (Crippen) 2.80
H-bond donors 2
H-bond acceptors 4
TPSA 57.50 Ų
Rotatable bonds 3
Aromatic rings 3 / 4
Heavy atoms 25
Fraction sp³ C 0.25
Formula C₂₀H₂₁N₃O₂

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 57.5
  • −1 ≤ LogP ≤ 5 2.80
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 335.4
  • LogP ≤ 5 2.80
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 57.5
PAINS Alert

Matches PAINS filter: indol_3yl_alk(461). May be a frequent false positive in HTS — review carefully.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CN1CCc2c(n(Cc3ccc(C(=O)NO)cc3)c3ccccc23)C1
InChI 
InChI=1S/C20H21N3O2/c1-22-11-10-17-16-4-2-3-5-18(16)23(19(17)13-22)12-14-6-8-15(9-7-14)20(24)21-25/h2-9,25H,10-13H2,1H3,(H,21,24)
InChIKey 
JVELXRPQMVXDDP-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
N9W
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)