Ligand profile

CHEMBL2165064

Bioactivity hit from ChEMBL on a similar protein.

Bound to: KP13_02784 — DNA topoisomerase 4 subunit A

Via homolog UniProt P20831 Formula C₂₅H₂₆FN₅O₃
pchembl 7.52 ~30.2 nM
Mol. weight 463.51 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL2165064
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 463.51 Da
LogP (Crippen) 2.24
H-bond donors 1
H-bond acceptors 8
TPSA 92.41 Ų
Rotatable bonds 6
Aromatic rings 3 / 5
Heavy atoms 34
Fraction sp³ C 0.40
Formula C₂₅H₂₆FN₅O₃

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 92.4
  • −1 ≤ LogP ≤ 5 2.24
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 463.5
  • LogP ≤ 5 2.24
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 8
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 92.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
N#Cc1ccc2ccc(=O)n(CCN3CC[C@H](NCc4cc5c(cn4)OCCO5)[C@H](F)C3)c2c1
InChI 
InChI=1S/C25H26FN5O3/c26-20-16-30(7-8-31-22-11-17(13-27)1-2-18(22)3-4-25(31)32)6-5-21(20)29-14-19-12-23-24(15-28-19)34-10-9-33-23/h1-4,11-12,15,20-21,29H,5-10,14,16H2/t20-,21+/m1/s1
InChIKey 
JYJKOWWSKTWAJA-RTWAWAEBSA-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)