Ligand profile

CHEMBL4096623

Bioactivity hit from ChEMBL on a similar protein.

Bound to: KP13_03495 — Histone deacetylase superfamily protein

Via homolog UniProt Q9Z2V5 Formula C₂₂H₃₄N₆O₃

Mol. weight 430.55 Da

Permeability Check

PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID: CHEMBL4096623
UniProt (similar protein): Q9Z2V5
Target protein: KP13_03495

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 430.55 Da

LogP (Crippen) 2.47

H-bond donors 3

H-bond acceptors 7

TPSA 112.38 Å²

Rotatable bonds 14

Aromatic rings 2 / 2

Heavy atoms 31

Fraction sp³ C 0.55

Formula C₂₂H₃₄N₆O₃

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 Å² and −1 ≤ LogP ≤ 5 are treated as a favorable small-molecule permeability screen.

TPSA ≤ 90 Å² 112.4
−1 ≤ LogP ≤ 5 2.47

Lipinski's Rule of Five Pass 0 violations

MW ≤ 500 Da 430.6
LogP ≤ 5 2.47
H-bond donors ≤ 5 3
H-bond acceptors ≤ 10 7

Veber's rules Fail

Rotatable bonds ≤ 10 14
TPSA ≤ 140 Å² 112.4

PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES

CCN(CC)CCNC(=O)c1ccc(-c2cn(CCCCCCC(=O)NO)nn2)cc1

InChI

InChI=1S/C22H34N6O3/c1-3-27(4-2)16-14-23-22(30)19-12-10-18(11-13-19)20-17-28(26-24-20)15-8-6-5-7-9-21(29)25-31/h10-13,17,31H,3-9,14-16H2,1-2H3,(H,23,30)(H,25,29)

InChIKey

WNNBSMMLUSHSMC-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.

ChEMBL ChEMBL compound CHEMBL4096623 →
UniProt UniProt Q9Z2V5 (homolog) →
PubChem PubChem (by InChIKey) →
Cheminformatics SwissADME prediction →
Cheminformatics SwissTargetPrediction →
Web Google Scholar (search “CHEMBL4096623”) →

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)