Ligand profile

55G

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

Bound to: KP13_00051 — DNA gyrase subunit B

Via homolog PDB 5ctx UniProt P0A0K8 Formula C₂₀H₁₃N₅OS
Mol. weight 371.43 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
55G
PDB
5ctx
UniProt (similar protein)
P0A0K8
Target protein
KP13_00051

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 371.43 Da
LogP (Crippen) 4.10
H-bond donors 2
H-bond acceptors 5
TPSA 87.32 Ų
Rotatable bonds 3
Aromatic rings 5 / 5
Heavy atoms 27
Fraction sp³ C 0.00
Formula C₂₀H₁₃N₅OS

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 87.3
  • −1 ≤ LogP ≤ 5 4.10
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 371.4
  • LogP ≤ 5 4.10
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 87.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1ccc(cc1)C2=CC(=O)Nc3c2c([nH]n3)c4cnc(s4)c5cccnc5
InChI 
InChI=1S/C20H13N5OS/c26-16-9-14(12-5-2-1-3-6-12)17-18(24-25-19(17)23-16)15-11-22-20(27-15)13-7-4-8-21-10-13/h1-11H,(H2,23,24,25,26)
InChIKey 
GPTXKTBHBIQZEL-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)