Ligand profile

CHEMBL2059373

Bioactivity hit from ChEMBL on a similar protein.

Bound to: KP13_00051 — DNA gyrase subunit B

Via homolog UniProt P0A0K8 Formula C₂₁H₁₅F₃N₆O₃
pchembl 7.41 ~38.9 nM
Mol. weight 456.38 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL2059373
UniProt (similar protein)
P0A0K8
pchembl
7.410 (~38.9 nM)
Target protein
KP13_00051

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 456.38 Da
LogP (Crippen) 3.42
H-bond donors 3
H-bond acceptors 6
TPSA 125.79 Ų
Rotatable bonds 5
Aromatic rings 4 / 5
Heavy atoms 33
Fraction sp³ C 0.19
Formula C₂₁H₁₅F₃N₆O₃

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 125.8
  • −1 ≤ LogP ≤ 5 3.42
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 456.4
  • LogP ≤ 5 3.42
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 125.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
O=C(O)c1cncc(-c2cnc3[nH]c(C(=O)NC4CC4)cc3c2-n2ccc(C(F)(F)F)n2)c1
InChI 
InChI=1S/C21H15F3N6O3/c22-21(23,24)16-3-4-30(29-16)17-13-6-15(19(31)27-12-1-2-12)28-18(13)26-9-14(17)10-5-11(20(32)33)8-25-7-10/h3-9,12H,1-2H2,(H,26,28)(H,27,31)(H,32,33)
InChIKey 
RQFOOLLFBDPYCK-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
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)