Ligand profile

9JN

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

Bound to: KP13_00051 — DNA gyrase subunit B

Via homolog PDB 5npk UniProt P66937 Formula C₂₀H₁₈N₄OS
Mol. weight 362.46 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
9JN
PDB
5npk
UniProt (similar protein)
P66937
Target protein
KP13_00051

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 362.46 Da
LogP (Crippen) 3.72
H-bond donors 3
H-bond acceptors 4
TPSA 83.80 Ų
Rotatable bonds 5
Aromatic rings 4 / 4
Heavy atoms 26
Fraction sp³ C 0.10
Formula C₂₀H₁₈N₄OS

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 83.8
  • −1 ≤ LogP ≤ 5 3.72
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 362.5
  • LogP ≤ 5 3.72
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 83.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1ccc(cc1)[C@@H](CN)NC(=O)c2cc(cs2)c3c[nH]c4c3cccn4
InChI 
InChI=1S/C20H18N4OS/c21-10-17(13-5-2-1-3-6-13)24-20(25)18-9-14(12-26-18)16-11-23-19-15(16)7-4-8-22-19/h1-9,11-12,17H,10,21H2,(H,22,23)(H,24,25)/t17-/m1/s1
InChIKey 
ZNBOMXQVNVLXCZ-QGZVFWFLSA-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
PF00521' 'PF01751

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)