Ligand profile

CHEMBL3808760

Bioactivity hit from ChEMBL on a similar protein.

Bound to: KP13_00051 — DNA gyrase subunit B

Via homolog UniProt P0A0K8 Formula C₂₀H₂₀N₆O₂S
pchembl 7.89 ~12.9 nM
Mol. weight 408.49 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL3808760
UniProt (similar protein)
P0A0K8
pchembl
7.890 (~12.9 nM)
Target protein
KP13_00051

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 408.49 Da
LogP (Crippen) 3.02
H-bond donors 1
H-bond acceptors 7
TPSA 96.77 Ų
Rotatable bonds 5
Aromatic rings 4 / 4
Heavy atoms 29
Fraction sp³ C 0.25
Formula C₂₀H₂₀N₆O₂S

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 96.8
  • −1 ≤ LogP ≤ 5 3.02
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 408.5
  • LogP ≤ 5 3.02
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 7
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 96.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCCn1c(=O)ccc2c(-c3nc(C(=O)N(C)C)c(-c4cccnc4)s3)n[nH]c21
InChI 
InChI=1S/C20H20N6O2S/c1-4-10-26-14(27)8-7-13-15(23-24-18(13)26)19-22-16(20(28)25(2)3)17(29-19)12-6-5-9-21-11-12/h5-9,11H,4,10H2,1-3H3,(H,23,24)
InChIKey 
GTYFFCZDHXHKMT-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)