Ligand profile

P5Y

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

Bound to: KP13_03495 — Histone deacetylase superfamily protein

Via homolog PDB 6pye UniProt F8W4B7 Formula C₂₅H₂₁F₃N₆O₃
Mol. weight 510.48 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
P5Y
PDB
6pye
UniProt (similar protein)
F8W4B7
Target protein
KP13_03495

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 510.48 Da
LogP (Crippen) 3.70
H-bond donors 2
H-bond acceptors 7
TPSA 113.24 Ų
Rotatable bonds 8
Aromatic rings 4 / 4
Heavy atoms 37
Fraction sp³ C 0.16
Formula C₂₅H₂₁F₃N₆O₃

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 113.2
  • −1 ≤ LogP ≤ 5 3.70
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 510.5
  • LogP ≤ 5 3.70
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 7
Veber's rules Pass
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 113.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1ccc(cc1)Cn2c(nnn2)CN(Cc3ccc(cc3)C(=O)NO)C(=O)c4ccccc4C(F)(F)F
InChI 
InChI=1S/C25H21F3N6O3/c26-25(27,28)21-9-5-4-8-20(21)24(36)33(14-18-10-12-19(13-11-18)23(35)30-37)16-22-29-31-32-34(22)15-17-6-2-1-3-7-17/h1-13,37H,14-16H2,(H,30,35)
InChIKey 
MEWDNULKAXEKII-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)