Ligand profile

CHEMBL4170768

Bioactivity hit from ChEMBL on a similar protein.

Bound to: KP13_03495 — Histone deacetylase superfamily protein

Via homolog UniProt Q9Z2V5 Formula C₂₀H₂₃N₅O₃
Mol. weight 381.44 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL4170768
UniProt (similar protein)
Q9Z2V5
Target protein
KP13_03495

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 381.44 Da
LogP (Crippen) 3.52
H-bond donors 4
H-bond acceptors 4
TPSA 110.35 Ų
Rotatable bonds 7
Aromatic rings 3 / 3
Heavy atoms 28
Fraction sp³ C 0.25
Formula C₂₀H₂₃N₅O₃

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 110.4
  • −1 ≤ LogP ≤ 5 3.52
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 381.4
  • LogP ≤ 5 3.52
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 110.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCCCN(Cc1ccc(C(=O)NO)cc1)C(=O)Nc1ccc2cn[nH]c2c1
InChI 
InChI=1S/C20H23N5O3/c1-2-3-10-25(13-14-4-6-15(7-5-14)19(26)24-28)20(27)22-17-9-8-16-12-21-23-18(16)11-17/h4-9,11-12,28H,2-3,10,13H2,1H3,(H,21,23)(H,22,27)(H,24,26)
InChIKey 
SDIVUCIYBAWAQP-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)