Ligand profile

CHEMBL4293447

Bioactivity hit from ChEMBL on a similar protein.

Bound to: KP13_00051 — DNA gyrase subunit B

Via homolog UniProt P0AES6 Formula C₂₅H₂₅F₃N₈OS
pchembl 8.22 ~6.0 nM
Mol. weight 542.59 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL4293447
UniProt (similar protein)
P0AES6
pchembl
8.220 (~6.0 nM)
Target protein
KP13_00051

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 542.59 Da
LogP (Crippen) 4.90
H-bond donors 3
H-bond acceptors 8
TPSA 121.95 Ų
Rotatable bonds 5
Aromatic rings 4 / 5
Heavy atoms 38
Fraction sp³ C 0.32
Formula C₂₅H₂₅F₃N₈OS

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 121.9
  • −1 ≤ LogP ≤ 5 4.90
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 542.6
  • LogP ≤ 5 4.90
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 8
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 121.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCNC(=O)Nc1cc(-c2nc(C(F)(F)F)cs2)c(-c2cc3ncccc3nc2N2CCC(N)CC2)cn1
InChI 
InChI=1S/C25H25F3N8OS/c1-2-30-24(37)35-21-11-16(23-34-20(13-38-23)25(26,27)28)17(12-32-21)15-10-19-18(4-3-7-31-19)33-22(15)36-8-5-14(29)6-9-36/h3-4,7,10-14H,2,5-6,8-9,29H2,1H3,(H2,30,32,35,37)
InChIKey 
GFCYSWOAOCSVFR-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
PF02518

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_00051.

PDB 88

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

Ligand PDB entry

ChEMBL 99

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)