Ligand profile

A6I

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

Bound to: KP13_03495 — Histone deacetylase superfamily protein

Via homolog PDB 6pzu UniProt F8W4B7 Formula C₂₅H₃₂N₄O₆
Mol. weight 484.55 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
A6I
PDB
6pzu
UniProt (similar protein)
F8W4B7
Target protein
KP13_03495

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 484.55 Da
LogP (Crippen) 2.27
H-bond donors 5
H-bond acceptors 6
TPSA 145.86 Ų
Rotatable bonds 11
Aromatic rings 2 / 2
Heavy atoms 35
Fraction sp³ C 0.36
Formula C₂₅H₃₂N₄O₆

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 145.9
  • −1 ≤ LogP ≤ 5 2.27
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 484.6
  • LogP ≤ 5 2.27
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 6
Veber's rules Fail
  • Rotatable bonds ≤ 10 11
  • TPSA ≤ 140 Ų 145.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@@H](C(=O)NCc1ccc(cc1)C(=O)NO)NC(=O)[C@H](CC(C)C)NC(=O)OCc2ccccc2
InChI 
InChI=1S/C25H32N4O6/c1-16(2)13-21(28-25(33)35-15-19-7-5-4-6-8-19)24(32)27-17(3)22(30)26-14-18-9-11-20(12-10-18)23(31)29-34/h4-12,16-17,21,34H,13-15H2,1-3H3,(H,26,30)(H,27,32)(H,28,33)(H,29,31)/t17-,21-/m0/s1
InChIKey 
YPOCKHLJSRDPHY-UWJYYQICSA-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)