Ligand profile

F1Y

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

Bound to: KP13_03495 — Histone deacetylase superfamily protein

Via homolog PDB 6cgp UniProt A7YT55 Formula C₁₇H₁₈N₄O₂
Mol. weight 310.36 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
F1Y
PDB
6cgp
UniProt (similar protein)
A7YT55
Target protein
KP13_03495

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 310.36 Da
LogP (Crippen) 3.15
H-bond donors 3
H-bond acceptors 5
TPSA 78.66 Ų
Rotatable bonds 5
Aromatic rings 3 / 3
Heavy atoms 23
Fraction sp³ C 0.18
Formula C₁₇H₁₈N₄O₂

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 78.7
  • −1 ≤ LogP ≤ 5 3.15
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 310.4
  • LogP ≤ 5 3.15
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 78.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCCc1c(n2ccccc2n1)Nc3ccc(cc3)C(=O)NO
InChI 
InChI=1S/C17H18N4O2/c1-2-5-14-16(21-11-4-3-6-15(21)19-14)18-13-9-7-12(8-10-13)17(22)20-23/h3-4,6-11,18,23H,2,5H2,1H3,(H,20,22)
InChIKey 
RDGVRQVQYOOAEK-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)