Ligand profile

CHEMBL5189146

Bioactivity hit from ChEMBL on a similar protein.

Bound to: KP13_03495 — Histone deacetylase superfamily protein

Via homolog UniProt Q9Z2V5 Formula C₂₅H₂₇N₃O₂
pchembl 6.96 ~109.6 nM
Mol. weight 401.51 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL5189146
UniProt (similar protein)
Q9Z2V5
pchembl
6.960 (~109.6 nM)
Target protein
KP13_03495

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 401.51 Da
LogP (Crippen) 3.71
H-bond donors 2
H-bond acceptors 4
TPSA 55.81 Ų
Rotatable bonds 6
Aromatic rings 3 / 4
Heavy atoms 30
Fraction sp³ C 0.24
Formula C₂₅H₂₇N₃O₂

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 55.8
  • −1 ≤ LogP ≤ 5 3.71
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 401.5
  • LogP ≤ 5 3.71
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 55.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
O=C(NO)c1ccc(CN2CCN(C(c3ccccc3)c3ccccc3)CC2)cc1
InChI 
InChI=1S/C25H27N3O2/c29-25(26-30)23-13-11-20(12-14-23)19-27-15-17-28(18-16-27)24(21-7-3-1-4-8-21)22-9-5-2-6-10-22/h1-14,24,30H,15-19H2,(H,26,29)
InChIKey 
WYZGPGZJNOPQLB-UHFFFAOYSA-N

Provenance

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

Method
LigQ nearest_k
Source
ChEMBL
Curation
pdb_similarity_tanimoto
Binding sites
PF00850

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 54

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 50

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

Compound Similarity (Tanimoto)