Ligand profile

55H

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

Bound to: KP13_00051 — DNA gyrase subunit B

Via homolog PDB 5cty UniProt P0A0K8 Formula C₁₄H₉N₅OS
Mol. weight 295.33 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
55H
PDB
5cty
UniProt (similar protein)
P0A0K8
Target protein
KP13_00051

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 295.33 Da
LogP (Crippen) 2.44
H-bond donors 2
H-bond acceptors 5
TPSA 87.32 Ų
Rotatable bonds 2
Aromatic rings 4 / 4
Heavy atoms 21
Fraction sp³ C 0.00
Formula C₁₄H₉N₅OS

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 2.44
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 295.3
  • LogP ≤ 5 2.44
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 87.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc(cnc1)c2ncc(s2)c3c4c(n[nH]3)NC(=O)C=C4
InChI 
InChI=1S/C14H9N5OS/c20-11-4-3-9-12(18-19-13(9)17-11)10-7-16-14(21-10)8-2-1-5-15-6-8/h1-7H,(H2,17,18,19,20)
InChIKey 
JCIZDZAGSUATFA-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)