Ligand profile

CHEMBL3809278

Bioactivity hit from ChEMBL on a similar protein.

Bound to: KP13_00051 — DNA gyrase subunit B

Via homolog UniProt P0A0K8 Formula C₂₀H₂₀N₆O₂S
pchembl 8.10 ~7.9 nM
Mol. weight 408.49 Da
Permeability Check
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL3809278
UniProt (similar protein)
P0A0K8
pchembl
8.100 (~7.9 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 Alert

Matches PAINS filter: dyes5A(27). May be a frequent false positive in HTS — review carefully.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCCn1c(=O)ccc2c(-c3cnc(-c4ccc(C(=O)N(C)C)nc4)s3)n[nH]c21
InChI 
InChI=1S/C20H20N6O2S/c1-4-9-26-16(27)8-6-13-17(23-24-18(13)26)15-11-22-19(29-15)12-5-7-14(21-10-12)20(28)25(2)3/h5-8,10-11H,4,9H2,1-3H3,(H,23,24)
InChIKey 
OWVRCTLRAWWWOH-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)