Ligand profile

E0F

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

Bound to: KP13_00051 — DNA gyrase subunit B

Via homolog PDB 6kzv UniProt P0AES6 Formula C₂₄H₂₇N₃O₂
Mol. weight 389.50 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
E0F
PDB
6kzv
UniProt (similar protein)
P0AES6
Target protein
KP13_00051

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 389.50 Da
LogP (Crippen) 4.54
H-bond donors 2
H-bond acceptors 3
TPSA 65.20 Ų
Rotatable bonds 5
Aromatic rings 3 / 4
Heavy atoms 29
Fraction sp³ C 0.33
Formula C₂₄H₂₇N₃O₂

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 65.2
  • −1 ≤ LogP ≤ 5 4.54
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 389.5
  • LogP ≤ 5 4.54
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 65.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CN(Cc1ccccc1NC(=O)C2=Cc3ccccc3NC2=O)C4CCCCC4
InChI 
InChI=1S/C24H27N3O2/c1-27(19-11-3-2-4-12-19)16-18-10-6-8-14-22(18)26-24(29)20-15-17-9-5-7-13-21(17)25-23(20)28/h5-10,13-15,19H,2-4,11-12,16H2,1H3,(H,25,28)(H,26,29)
InChIKey 
HXOAPOMHVOADBB-UHFFFAOYSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ sequence
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)