Ligand profile

ZINC108646681

Virtual-screening candidate from ZINC.

Bound to: KP13_03495 — Histone deacetylase superfamily protein

Via homolog UniProt F8W4B7 Formula C₂₁H₂₂N₂O₂
Tanimoto 0.83
Mol. weight 334.42 Da
Permeability High
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC108646681
UniProt (similar protein)
F8W4B7
Tanimoto
0.827
Target protein
KP13_03495

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 334.42 Da
LogP (Crippen) 3.91
H-bond donors 3
H-bond acceptors 2
TPSA 65.12 Ų
Rotatable bonds 7
Aromatic rings 3 / 3
Heavy atoms 25
Fraction sp³ C 0.19
Formula C₂₁H₂₂N₂O₂

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 65.1
  • −1 ≤ LogP ≤ 5 3.91
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 334.4
  • LogP ≤ 5 3.91
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 2
Veber's rules Pass
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 65.1
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 
Cc1[nH]c2ccccc2c1CCNCc1ccc(/C=C/C(=O)O)cc1
InChI 
InChI=1S/C21H22N2O2/c1-15-18(19-4-2-3-5-20(19)23-15)12-13-22-14-17-8-6-16(7-9-17)10-11-21(24)25/h2-11,22-23H,12-14H2,1H3,(H,24,25)/b11-10+
InChIKey 
XVXVAVCOKYEXMZ-ZHACJKMWSA-N

Provenance

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

Method
LigQ nearest_k
Query
LBH
Homolog
F8W4B7

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)