Ligand profile

CHEMBL4867598

Bioactivity hit from ChEMBL on a similar protein.

Bound to: KP13_03495 — Histone deacetylase superfamily protein

Via homolog UniProt Q9Z2V5 Formula C₂₀H₁₈N₄O₄
Mol. weight 378.39 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL4867598
UniProt (similar protein)
Q9Z2V5
Target protein
KP13_03495

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 378.39 Da
LogP (Crippen) 2.48
H-bond donors 4
H-bond acceptors 6
TPSA 112.05 Ų
Rotatable bonds 5
Aromatic rings 2 / 4
Heavy atoms 28
Fraction sp³ C 0.15
Formula C₂₀H₁₈N₄O₄

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 112.0
  • −1 ≤ LogP ≤ 5 2.48
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 378.4
  • LogP ≤ 5 2.48
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 112.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
O=C(CCCO/N=C1C(=C2/C(=O)Nc3ccccc32)/Nc2ccccc2/1)NO
InChI 
InChI=1S/C20H18N4O4/c25-16(23-27)10-5-11-28-24-18-13-7-2-4-9-15(13)21-19(18)17-12-6-1-3-8-14(12)22-20(17)26/h1-4,6-9,21,27H,5,10-11H2,(H,22,26)(H,23,25)/b19-17-,24-18+
InChIKey 
PFMKIDRZHBZULH-FTCCNZMVSA-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)