Ligand profile

CHEMBL3809648

Bioactivity hit from ChEMBL on a similar protein.

Bound to: KP13_00051 — DNA gyrase subunit B

Via homolog UniProt P0A0K8 Formula C₂₃H₂₇N₇OS
pchembl 8.00 ~10.0 nM
Mol. weight 449.58 Da
Permeability High
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL3809648
UniProt (similar protein)
P0A0K8
pchembl
8.000 (~10.0 nM)
Target protein
KP13_00051

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 449.58 Da
LogP (Crippen) 3.07
H-bond donors 1
H-bond acceptors 8
TPSA 82.94 Ų
Rotatable bonds 6
Aromatic rings 4 / 5
Heavy atoms 32
Fraction sp³ C 0.39
Formula C₂₃H₂₇N₇OS

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy High

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 82.9
  • −1 ≤ LogP ≤ 5 3.07
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 449.6
  • LogP ≤ 5 3.07
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 8
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 82.9
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(CN5CCN(C)CC5)nc4)s3)n[nH]c21
InChI 
InChI=1S/C23H27N7OS/c1-3-8-30-20(31)7-6-18-21(26-27-22(18)30)19-14-25-23(32-19)16-4-5-17(24-13-16)15-29-11-9-28(2)10-12-29/h4-7,13-14H,3,8-12,15H2,1-2H3,(H,26,27)
InChIKey 
ZXFXGNACVGPULM-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)