Ligand profile

A8K

Ligand co-crystallized with a similar protein (Protein Data Bank).

Bound to: KP13_00051 — DNA gyrase subunit B

Via homolog PDB 5z4h UniProt P0AES6 Formula C₁₂H₁₀O₂S
Mol. weight 218.28 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
A8K
PDB
5z4h
UniProt (similar protein)
P0AES6
Target protein
KP13_00051

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 218.28 Da
LogP (Crippen) 3.25
H-bond donors 2
H-bond acceptors 3
TPSA 40.46 Ų
Rotatable bonds 2
Aromatic rings 2 / 2
Heavy atoms 15
Fraction sp³ C 0.00
Formula C₁₂H₁₀O₂S

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 40.5
  • −1 ≤ LogP ≤ 5 3.25
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 218.3
  • LogP ≤ 5 3.25
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 40.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc(ccc1O)Sc2ccc(cc2)O
InChI 
InChI=1S/C12H10O2S/c13-9-1-5-11(6-2-9)15-12-7-3-10(14)4-8-12/h1-8,13-14H
InChIKey 
VWGKEVWFBOUAND-UHFFFAOYSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ sequence
Source
PDB
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 87

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ChEMBL 100

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)