Ligand profile

HBG

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

Bound to: KP13_03495 — Histone deacetylase superfamily protein

Via homolog PDB 6dvl UniProt F8W4B7 Formula C₂₅H₃₁N₃O₄
Mol. weight 437.54 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
HBG
PDB
6dvl
UniProt (similar protein)
F8W4B7
Target protein
KP13_03495

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 437.54 Da
LogP (Crippen) 3.51
H-bond donors 3
H-bond acceptors 4
TPSA 98.74 Ų
Rotatable bonds 7
Aromatic rings 2 / 3
Heavy atoms 32
Fraction sp³ C 0.40
Formula C₂₅H₃₁N₃O₄

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 98.7
  • −1 ≤ LogP ≤ 5 3.51
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 437.5
  • LogP ≤ 5 3.51
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 98.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1cc(cc(c1)C(=O)N(Cc2ccc(cc2)C(=O)NO)CC(=O)NC3CCCCC3)C
InChI 
InChI=1S/C25H31N3O4/c1-17-12-18(2)14-21(13-17)25(31)28(16-23(29)26-22-6-4-3-5-7-22)15-19-8-10-20(11-9-19)24(30)27-32/h8-14,22,32H,3-7,15-16H2,1-2H3,(H,26,29)(H,27,30)
InChIKey 
PEXKZGDNGWXGSQ-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)