Ligand profile

CHEMBL4530328

Bioactivity hit from ChEMBL on a similar protein.

Bound to: KP13_02784 — DNA topoisomerase 4 subunit A

Via homolog UniProt P0AFI2 Formula C₂₄H₂₄FN₅O₃
pchembl 6.40 ~398.1 nM
Mol. weight 449.49 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL4530328
UniProt (similar protein)
P0AFI2
pchembl
6.400 (~398.1 nM)
Target protein
KP13_02784

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 449.49 Da
LogP (Crippen) 2.47
H-bond donors 2
H-bond acceptors 8
TPSA 94.73 Ų
Rotatable bonds 6
Aromatic rings 4 / 5
Heavy atoms 33
Fraction sp³ C 0.29
Formula C₂₄H₂₄FN₅O₃

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 94.7
  • −1 ≤ LogP ≤ 5 2.47
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 449.5
  • LogP ≤ 5 2.47
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 8
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 94.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
O=c1nc(NC[C@@H](O)CN2CCN(c3nccc4ccc(F)cc34)CC2)c2ccccc2o1
InChI 
InChI=1S/C24H24FN5O3/c25-17-6-5-16-7-8-26-23(20(16)13-17)30-11-9-29(10-12-30)15-18(31)14-27-22-19-3-1-2-4-21(19)33-24(32)28-22/h1-8,13,18,31H,9-12,14-15H2,(H,27,28,32)/t18-/m1/s1
InChIKey 
ILSQZDCVJPCWKM-GOSISDBHSA-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)