Ligand profile

E3E

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

Bound to: KP13_00051 — DNA gyrase subunit B

Via homolog PDB 6fqs UniProt P66937 Formula C₁₈H₁₃FN₄O
Mol. weight 320.33 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
E3E
PDB
6fqs
UniProt (similar protein)
P66937
Target protein
KP13_00051

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 320.33 Da
LogP (Crippen) 3.19
H-bond donors 0
H-bond acceptors 5
TPSA 52.19 Ų
Rotatable bonds 2
Aromatic rings 4 / 5
Heavy atoms 24
Fraction sp³ C 0.17
Formula C₁₈H₁₃FN₄O

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 52.2
  • −1 ≤ LogP ≤ 5 3.19
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 320.3
  • LogP ≤ 5 3.19
  • H-bond donors ≤ 5 0
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 52.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cnccc1c2cc3c(cc2F)-n4ccnc4C(=O)N3C5CC5
InChI 
InChI=1S/C18H13FN4O/c19-14-10-15-16(9-13(14)11-3-5-20-6-4-11)23(12-1-2-12)18(24)17-21-7-8-22(15)17/h3-10,12H,1-2H2
InChIKey 
UZAPAHIWOLYIFO-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
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)