Ligand profile

HBJ

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

Bound to: KP13_03495 — Histone deacetylase superfamily protein

Via homolog PDB 6dvm UniProt F8W4B7 Formula C₂₆H₂₈N₄O₄
Mol. weight 460.53 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
HBJ
PDB
6dvm
UniProt (similar protein)
F8W4B7
Target protein
KP13_03495

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 460.53 Da
LogP (Crippen) 3.46
H-bond donors 3
H-bond acceptors 5
TPSA 101.98 Ų
Rotatable bonds 8
Aromatic rings 3 / 3
Heavy atoms 34
Fraction sp³ C 0.19
Formula C₂₆H₂₈N₄O₄

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 102.0
  • −1 ≤ LogP ≤ 5 3.46
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 460.5
  • LogP ≤ 5 3.46
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 102.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1ccc(cc1)NC(=O)CN(Cc2ccc(cc2)C(=O)NO)C(=O)c3ccc(cc3)N(C)C
InChI 
InChI=1S/C26H28N4O4/c1-18-4-12-22(13-5-18)27-24(31)17-30(16-19-6-8-20(9-7-19)25(32)28-34)26(33)21-10-14-23(15-11-21)29(2)3/h4-15,34H,16-17H2,1-3H3,(H,27,31)(H,28,32)
InChIKey 
UEKPDDMOEDHDCS-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)