Ligand profile

CHEMBL5175813

Bioactivity hit from ChEMBL on a similar protein.

Bound to: KP13_03495 — Histone deacetylase superfamily protein

Via homolog UniProt Q9Z2V5 Formula C₂₈H₃₃N₃O₂
pchembl 6.37 ~426.6 nM
Mol. weight 443.59 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL5175813
UniProt (similar protein)
Q9Z2V5
pchembl
6.370 (~426.6 nM)
Target protein
KP13_03495

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 443.59 Da
LogP (Crippen) 4.54
H-bond donors 2
H-bond acceptors 4
TPSA 55.81 Ų
Rotatable bonds 9
Aromatic rings 3 / 4
Heavy atoms 33
Fraction sp³ C 0.32
Formula C₂₈H₃₃N₃O₂

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 4.54
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 443.6
  • LogP ≤ 5 4.54
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 55.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
O=C(NO)c1ccc(CCCCN2CCN(C(c3ccccc3)c3ccccc3)CC2)cc1
InChI 
InChI=1S/C28H33N3O2/c32-28(29-33)26-16-14-23(15-17-26)9-7-8-18-30-19-21-31(22-20-30)27(24-10-3-1-4-11-24)25-12-5-2-6-13-25/h1-6,10-17,27,33H,7-9,18-22H2,(H,29,32)
InChIKey 
VESYDOZDDMFQMJ-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)