Ligand profile

54X

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

Bound to: KP13_00051 — DNA gyrase subunit B

Via homolog PDB 5ctu UniProt P0A0K8 Formula C₁₀H₆N₂OS₂
Mol. weight 234.30 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
54X
PDB
5ctu
UniProt (similar protein)
P0A0K8
Target protein
KP13_00051

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 234.30 Da
LogP (Crippen) 2.71
H-bond donors 1
H-bond acceptors 4
TPSA 45.75 Ų
Rotatable bonds 1
Aromatic rings 3 / 3
Heavy atoms 15
Fraction sp³ C 0.00
Formula C₁₀H₆N₂OS₂

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 45.8
  • −1 ≤ LogP ≤ 5 2.71
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 234.3
  • LogP ≤ 5 2.71
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 1
  • TPSA ≤ 140 Ų 45.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc(sc1)c2csc3c2C(=O)N=CN3
InChI 
InChI=1S/C10H6N2OS2/c13-9-8-6(7-2-1-3-14-7)4-15-10(8)12-5-11-9/h1-5H,(H,11,12,13)
InChIKey 
LFUBTAOTPHKKOS-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
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)