Ligand profile

CHEMBL2424894

Bioactivity hit from ChEMBL on a similar protein.

Bound to: KP13_02784 — DNA topoisomerase 4 subunit A

Via homolog UniProt P20831 Formula C₂₅H₂₇FN₄O₃
pchembl 7.52 ~30.2 nM
Mol. weight 450.51 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL2424894
UniProt (similar protein)
P20831
pchembl
7.520 (~30.2 nM)
Target protein
KP13_02784

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 450.51 Da
LogP (Crippen) 2.66
H-bond donors 1
H-bond acceptors 7
TPSA 68.62 Ų
Rotatable bonds 5
Aromatic rings 3 / 6
Heavy atoms 33
Fraction sp³ C 0.44
Formula C₂₅H₂₇FN₄O₃

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 68.6
  • −1 ≤ LogP ≤ 5 2.66
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 450.5
  • LogP ≤ 5 2.66
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 7
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 68.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
O=c1ccc2ccc(F)c3c2n1CC3CN1CCC(NCc2cc3c(cn2)OCCO3)CC1
InChI 
InChI=1S/C25H27FN4O3/c26-20-3-1-16-2-4-23(31)30-15-17(24(20)25(16)30)14-29-7-5-18(6-8-29)27-12-19-11-21-22(13-28-19)33-10-9-32-21/h1-4,11,13,17-18,27H,5-10,12,14-15H2
InChIKey 
AUXHQPYDIVPJQT-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
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)