Ligand profile

CHEMBL1934904

Bioactivity hit from ChEMBL on a similar protein.

Bound to: KP13_03495 — Histone deacetylase superfamily protein

Via homolog UniProt Q70I53 Formula C₂₀H₁₂F₁₂N₂O₃
pchembl 6.35 ~446.7 nM
Mol. weight 556.30 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL1934904
UniProt (similar protein)
Q70I53
pchembl
6.350 (~446.7 nM)
Target protein
KP13_03495

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 556.30 Da
LogP (Crippen) 5.61
H-bond donors 3
H-bond acceptors 3
TPSA 78.43 Ų
Rotatable bonds 9
Aromatic rings 2 / 2
Heavy atoms 37
Fraction sp³ C 0.30
Formula C₂₀H₁₂F₁₂N₂O₃

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 78.4
  • −1 ≤ LogP ≤ 5 5.61
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 556.3
  • LogP ≤ 5 5.61
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 78.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
O=C(NO)C(F)(F)C(F)(F)C(F)(F)C(F)(F)C(F)(F)C(F)(F)C(=O)Nc1cccc(-c2ccccc2)c1
InChI 
InChI=1S/C20H12F12N2O3/c21-15(22,13(35)33-12-8-4-7-11(9-12)10-5-2-1-3-6-10)17(25,26)19(29,30)20(31,32)18(27,28)16(23,24)14(36)34-37/h1-9,37H,(H,33,35)(H,34,36)
InChIKey 
RFDGYNNXFQVRFM-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
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)