Ligand profile

CHEMBL2424893

Bioactivity hit from ChEMBL on a similar protein.

Bound to: KP13_02784 — DNA topoisomerase 4 subunit A

Via homolog UniProt P20831 Formula C₂₄H₂₆N₆O₃S
pchembl 8.10 ~7.9 nM
Mol. weight 478.58 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL2424893
UniProt (similar protein)
P20831
pchembl
8.100 (~7.9 nM)
Target protein
KP13_02784

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 478.58 Da
LogP (Crippen) 3.36
H-bond donors 3
H-bond acceptors 8
TPSA 118.13 Ų
Rotatable bonds 6
Aromatic rings 3 / 5
Heavy atoms 34
Fraction sp³ C 0.38
Formula C₂₄H₂₆N₆O₃S

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 118.1
  • −1 ≤ LogP ≤ 5 3.36
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 478.6
  • LogP ≤ 5 3.36
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 8
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 118.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
COc1ccc2nccc(NC(=O)[C@H]3CC[C@H](NCc4ccc5c(n4)NC(=O)CS5)CC3)c2n1
InChI 
InChI=1S/C24H26N6O3S/c1-33-21-9-7-17-22(30-21)18(10-11-25-17)28-24(32)14-2-4-15(5-3-14)26-12-16-6-8-19-23(27-16)29-20(31)13-34-19/h6-11,14-15,26H,2-5,12-13H2,1H3,(H,25,28,32)(H,27,29,31)/t14-,15-
InChIKey 
TVDNDLRKUKVCCR-SHTZXODSSA-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)