Ligand profile

CHEMBL4550214

Bioactivity hit from ChEMBL on a similar protein.

Bound to: KP13_03495 — Histone deacetylase superfamily protein

Via homolog UniProt Q9Z2V5 Formula C₂₄H₂₁N₃O₄
Mol. weight 415.45 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL4550214
UniProt (similar protein)
Q9Z2V5
Target protein
KP13_03495

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 415.45 Da
LogP (Crippen) 2.57
H-bond donors 2
H-bond acceptors 6
TPSA 93.33 Ų
Rotatable bonds 6
Aromatic rings 4 / 4
Heavy atoms 31
Fraction sp³ C 0.12
Formula C₂₄H₂₁N₃O₄

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy Check

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 93.3
  • −1 ≤ LogP ≤ 5 2.57
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 415.4
  • LogP ≤ 5 2.57
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 93.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
O=C(NO)c1ccc(Cn2c(=O)n(CCc3ccccc3)c(=O)c3ccccc32)cc1
InChI 
InChI=1S/C24H21N3O4/c28-22(25-31)19-12-10-18(11-13-19)16-27-21-9-5-4-8-20(21)23(29)26(24(27)30)15-14-17-6-2-1-3-7-17/h1-13,31H,14-16H2,(H,25,28)
InChIKey 
JBJIKUXUKSADFV-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
Activity
Active
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)