Ligand profile

B48

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

Bound to: KP13_00051 — DNA gyrase subunit B

Via homolog PDB 3g75 UniProt P0A0K8 Formula C₁₂H₁₁N₃S₃
Mol. weight 293.44 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
B48
PDB
3g75
UniProt (similar protein)
P0A0K8
Target protein
KP13_00051

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 293.44 Da
LogP (Crippen) 4.29
H-bond donors 1
H-bond acceptors 5
TPSA 41.57 Ų
Rotatable bonds 3
Aromatic rings 3 / 3
Heavy atoms 18
Fraction sp³ C 0.17
Formula C₁₂H₁₁N₃S₃

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 41.6
  • −1 ≤ LogP ≤ 5 4.29
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 293.4
  • LogP ≤ 5 4.29
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 41.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1c(sc(n1)c2cccs2)c3cc(n[nH]3)SC
InChI 
InChI=1S/C12H11N3S3/c1-7-11(8-6-10(16-2)15-14-8)18-12(13-7)9-4-3-5-17-9/h3-6H,1-2H3,(H,14,15)
InChIKey 
QVFLVBFBDVWAJG-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)