Ligand profile

P6Y

Ligand co-crystallized with a similar protein (Protein Data Bank).

Bound to: KP13_03495 — Histone deacetylase superfamily protein

Via homolog PDB 6pzo UniProt F8W4B7 Formula C₁₅H₁₂F₃N₃O₃
Mol. weight 339.27 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
P6Y
PDB
6pzo
UniProt (similar protein)
F8W4B7
Target protein
KP13_03495

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 339.27 Da
LogP (Crippen) 2.15
H-bond donors 3
H-bond acceptors 4
TPSA 91.32 Ų
Rotatable bonds 4
Aromatic rings 2 / 2
Heavy atoms 24
Fraction sp³ C 0.13
Formula C₁₅H₁₂F₃N₃O₃

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 91.3
  • −1 ≤ LogP ≤ 5 2.15
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 339.3
  • LogP ≤ 5 2.15
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 91.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc(c(nc1)C(F)(F)F)C(=O)NCc2ccc(cc2)C(=O)NO
InChI 
InChI=1S/C15H12F3N3O3/c16-15(17,18)12-11(2-1-7-19-12)14(23)20-8-9-3-5-10(6-4-9)13(22)21-24/h1-7,24H,8H2,(H,20,23)(H,21,22)
InChIKey 
SQBRKYYJEYSFMY-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
PDB
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 45

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ChEMBL 55

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)