Ligand profile

55D

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

Bound to: KP13_00051 — DNA gyrase subunit B

Via homolog PDB 5ctw UniProt P0A0K8 Formula C₉H₁₂N₂O₂S
Mol. weight 212.27 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
55D
PDB
5ctw
UniProt (similar protein)
P0A0K8
Target protein
KP13_00051

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 212.27 Da
LogP (Crippen) 1.59
H-bond donors 2
H-bond acceptors 3
TPSA 72.19 Ų
Rotatable bonds 4
Aromatic rings 1 / 1
Heavy atoms 14
Fraction sp³ C 0.33
Formula C₉H₁₂N₂O₂S

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 72.2
  • −1 ≤ LogP ≤ 5 1.59
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 212.3
  • LogP ≤ 5 1.59
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 72.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCCC(=O)Nc1c(ccs1)C(=O)N
InChI 
InChI=1S/C9H12N2O2S/c1-2-3-7(12)11-9-6(8(10)13)4-5-14-9/h4-5H,2-3H2,1H3,(H2,10,13)(H,11,12)
InChIKey 
QFUOJZBSCYPNSJ-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)