Ligand profile

CHEMBL5089854

Bioactivity hit from ChEMBL on a similar protein.

Bound to: KP13_03495 — Histone deacetylase superfamily protein

Via homolog UniProt Q9Z2V5 Formula C₂₀H₂₃N₃O₄S
Mol. weight 401.49 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL5089854
UniProt (similar protein)
Q9Z2V5
Target protein
KP13_03495

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 401.49 Da
LogP (Crippen) 2.44
H-bond donors 4
H-bond acceptors 5
TPSA 107.53 Ų
Rotatable bonds 10
Aromatic rings 2 / 2
Heavy atoms 28
Fraction sp³ C 0.25
Formula C₂₀H₂₃N₃O₄S

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 107.5
  • −1 ≤ LogP ≤ 5 2.44
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 401.5
  • LogP ≤ 5 2.44
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 10
  • TPSA ≤ 140 Ų 107.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
O=C(CCCSC[C@H](NC(=O)c1ccccc1)C(=O)Nc1ccccc1)NO
InChI 
InChI=1S/C20H23N3O4S/c24-18(23-27)12-7-13-28-14-17(20(26)21-16-10-5-2-6-11-16)22-19(25)15-8-3-1-4-9-15/h1-6,8-11,17,27H,7,12-14H2,(H,21,26)(H,22,25)(H,23,24)/t17-/m0/s1
InChIKey 
KLPIKEBAJICFPE-KRWDZBQOSA-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)