Ligand profile

E0R

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

Bound to: KP13_00051 — DNA gyrase subunit B

Via homolog PDB 6kzz UniProt P0AES6 Formula C₁₈H₁₅N₃O₄
Mol. weight 337.34 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
E0R
PDB
6kzz
UniProt (similar protein)
P0AES6
Target protein
KP13_00051

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 337.34 Da
LogP (Crippen) 2.52
H-bond donors 4
H-bond acceptors 4
TPSA 111.29 Ų
Rotatable bonds 4
Aromatic rings 3 / 3
Heavy atoms 25
Fraction sp³ C 0.06
Formula C₁₈H₁₅N₃O₄

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy Check

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 111.3
  • −1 ≤ LogP ≤ 5 2.52
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 337.3
  • LogP ≤ 5 2.52
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 111.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CNc1cccc2c1NC(=O)C(=C2)C(=O)Nc3ccc(cc3)C(=O)O
InChI 
InChI=1S/C18H15N3O4/c1-19-14-4-2-3-11-9-13(17(23)21-15(11)14)16(22)20-12-7-5-10(6-8-12)18(24)25/h2-9,19H,1H3,(H,20,22)(H,21,23)(H,24,25)
InChIKey 
VUXYPRAXFABKBH-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)