Ligand profile

6DK

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

Bound to: KP13_03495 — Histone deacetylase superfamily protein

Via homolog PDB 5g10 UniProt Q9HXM1 Formula C₁₅H₂₀F₃NO₃
Mol. weight 319.32 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
6DK
PDB
5g10
UniProt (similar protein)
Q9HXM1
Target protein
KP13_03495

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 319.32 Da
LogP (Crippen) 3.21
H-bond donors 3
H-bond acceptors 3
TPSA 69.56 Ų
Rotatable bonds 8
Aromatic rings 1 / 1
Heavy atoms 22
Fraction sp³ C 0.53
Formula C₁₅H₂₀F₃NO₃

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 69.6
  • −1 ≤ LogP ≤ 5 3.21
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 319.3
  • LogP ≤ 5 3.21
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 69.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1ccc(cc1)NC(=O)CCCCCCC(C(F)(F)F)(O)O
InChI 
InChI=1S/C15H20F3NO3/c16-15(17,18)14(21,22)11-7-2-1-6-10-13(20)19-12-8-4-3-5-9-12/h3-5,8-9,21-22H,1-2,6-7,10-11H2,(H,19,20)
InChIKey 
DOVGAPNVSPZBAT-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)