Ligand profile

CHEMBL4569403

Bioactivity hit from ChEMBL on a similar protein.

Bound to: KP13_02784 — DNA topoisomerase 4 subunit A

Via homolog UniProt P0AFI2 Formula C₂₆H₂₈N₄O₃
pchembl 6.05 ~891.3 nM
Mol. weight 444.54 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL4569403
UniProt (similar protein)
P0AFI2
pchembl
6.050 (~891.3 nM)
Target protein
KP13_02784

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 444.54 Da
LogP (Crippen) 3.97
H-bond donors 1
H-bond acceptors 7
TPSA 70.84 Ų
Rotatable bonds 7
Aromatic rings 4 / 5
Heavy atoms 33
Fraction sp³ C 0.31
Formula C₂₆H₂₈N₄O₃

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 70.8
  • −1 ≤ LogP ≤ 5 3.97
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 444.5
  • LogP ≤ 5 3.97
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 7
Veber's rules Pass
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 70.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
COc1ccc2ccnc(N3CCN(CCCNc4cc(=O)oc5ccccc45)CC3)c2c1
InChI 
InChI=1S/C26H28N4O3/c1-32-20-8-7-19-9-11-28-26(22(19)17-20)30-15-13-29(14-16-30)12-4-10-27-23-18-25(31)33-24-6-3-2-5-21(23)24/h2-3,5-9,11,17-18,27H,4,10,12-16H2,1H3
InChIKey 
YLKRJZMQGDSHIU-UHFFFAOYSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ sequence
Source
ChEMBL
Curation
pdb_similarity_tanimoto
Binding sites
PF00521

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_02784.

PDB 23

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ChEMBL 14

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)