Ligand profile

CHEMBL5172611

Bioactivity hit from ChEMBL on a similar protein.

Bound to: KP13_03495 — Histone deacetylase superfamily protein

Via homolog UniProt Q9Z2V5 Formula C₂₆H₂₉N₃O₂
pchembl 6.48 ~331.1 nM
Mol. weight 415.54 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL5172611
UniProt (similar protein)
Q9Z2V5
pchembl
6.480 (~331.1 nM)
Target protein
KP13_03495

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 415.54 Da
LogP (Crippen) 3.76
H-bond donors 2
H-bond acceptors 4
TPSA 55.81 Ų
Rotatable bonds 7
Aromatic rings 3 / 4
Heavy atoms 31
Fraction sp³ C 0.27
Formula C₂₆H₂₉N₃O₂

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 3.76
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 415.5
  • LogP ≤ 5 3.76
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 55.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
O=C(NO)c1ccc(CCN2CCN(C(c3ccccc3)c3ccccc3)CC2)cc1
InChI 
InChI=1S/C26H29N3O2/c30-26(27-31)24-13-11-21(12-14-24)15-16-28-17-19-29(20-18-28)25(22-7-3-1-4-8-22)23-9-5-2-6-10-23/h1-14,25,31H,15-20H2,(H,27,30)
InChIKey 
CJSCFEBBGAGVJI-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)