Ligand profile

ZINC2382315727

Virtual-screening candidate from ZINC.

Bound to: KP13_03495 — Histone deacetylase superfamily protein

Via homolog UniProt Q9Z2V5 Formula C₂₁H₂₃N₃O₂
Tanimoto 0.78
Mol. weight 349.43 Da
Permeability High
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC2382315727
UniProt (similar protein)
Q9Z2V5
Tanimoto
0.782
Target protein
KP13_03495

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 349.43 Da
LogP (Crippen) 3.10
H-bond donors 2
H-bond acceptors 4
TPSA 57.50 Ų
Rotatable bonds 3
Aromatic rings 3 / 4
Heavy atoms 26
Fraction sp³ C 0.29
Formula C₂₁H₂₃N₃O₂

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 3.10
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 349.4
  • LogP ≤ 5 3.10
  • 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 
Cc1cc(Cn2c3c(c4ccccc42)CN(C)CC3)ccc1C(=O)NO
InChI 
InChI=1S/C21H23N3O2/c1-14-11-15(7-8-16(14)21(25)22-26)12-24-19-6-4-3-5-17(19)18-13-23(2)10-9-20(18)24/h3-8,11,26H,9-10,12-13H2,1-2H3,(H,22,25)
InChIKey 
XDQCYFNRZUSCDW-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)