Ligand profile

CHEMBL3809816

Bioactivity hit from ChEMBL on a similar protein.

Bound to: KP13_00051 — DNA gyrase subunit B

Via homolog UniProt P0A0K8 Formula C₂₂H₂₆N₆OS
pchembl 8.05 ~8.9 nM
Mol. weight 422.56 Da
Permeability High
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL3809816
UniProt (similar protein)
P0A0K8
pchembl
8.050 (~8.9 nM)
Target protein
KP13_00051

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 422.56 Da
LogP (Crippen) 4.16
H-bond donors 1
H-bond acceptors 7
TPSA 79.70 Ų
Rotatable bonds 8
Aromatic rings 4 / 4
Heavy atoms 30
Fraction sp³ C 0.36
Formula C₂₂H₂₆N₆OS

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 79.7
  • −1 ≤ LogP ≤ 5 4.16
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 422.6
  • LogP ≤ 5 4.16
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 7
Veber's rules Pass
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 79.7
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(CN(CC)CC)nc4)s3)n[nH]c21
InChI 
InChI=1S/C22H26N6OS/c1-4-11-28-19(29)10-9-17-20(25-26-21(17)28)18-13-24-22(30-18)15-7-8-16(23-12-15)14-27(5-2)6-3/h7-10,12-13H,4-6,11,14H2,1-3H3,(H,25,26)
InChIKey 
RYWREJZREPBNEF-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)