Ligand profile

CHEMBL3739580

Bioactivity hit from ChEMBL on a similar protein.

Bound to: KP13_00051 — DNA gyrase subunit B

Via homolog UniProt P0A0K8 Formula C₂₁H₁₈FN₃O₃S
pchembl 7.82 ~15.1 nM
Mol. weight 411.46 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL3739580
UniProt (similar protein)
P0A0K8
pchembl
7.820 (~15.1 nM)
Target protein
KP13_00051

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 411.46 Da
LogP (Crippen) 5.15
H-bond donors 2
H-bond acceptors 5
TPSA 88.10 Ų
Rotatable bonds 6
Aromatic rings 4 / 4
Heavy atoms 29
Fraction sp³ C 0.19
Formula C₂₁H₁₈FN₃O₃S

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 88.1
  • −1 ≤ LogP ≤ 5 5.15
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 411.5
  • LogP ≤ 5 5.15
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 88.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCCc1c(OC)ccc2c(-c3cnc(-c4ccc(C(=O)O)c(F)c4)s3)n[nH]c12
InChI 
InChI=1S/C21H18FN3O3S/c1-3-4-13-16(28-2)8-7-14-18(13)24-25-19(14)17-10-23-20(29-17)11-5-6-12(21(26)27)15(22)9-11/h5-10H,3-4H2,1-2H3,(H,24,25)(H,26,27)
InChIKey 
ZSEPCNOMXOGSSY-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)