Ligand profile

EZ9

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

Bound to: KP13_00051 — DNA gyrase subunit B

Via homolog PDB 6m1s UniProt Q9I7C2 Formula C₂₆H₂₃F₄N₇O₃
Mol. weight 557.51 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
EZ9
PDB
6m1s
UniProt (similar protein)
Q9I7C2
Target protein
KP13_00051

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 557.51 Da
LogP (Crippen) 5.44
H-bond donors 3
H-bond acceptors 8
TPSA 130.84 Ų
Rotatable bonds 8
Aromatic rings 5 / 5
Heavy atoms 40
Fraction sp³ C 0.27
Formula C₂₆H₂₃F₄N₇O₃

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 130.8
  • −1 ≤ LogP ≤ 5 5.44
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 557.5
  • LogP ≤ 5 5.44
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 8
Veber's rules Pass
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 130.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCNc1cc(cc2c1[nH]c3c2c(c(cn3)c4cnc(nc4)OCC(C)(C)C(=O)O)n5ccc(n5)C(F)(F)F)F
InChI 
InChI=1S/C26H23F4N7O3/c1-4-31-17-8-14(27)7-15-19-21(37-6-5-18(36-37)26(28,29)30)16(11-32-22(19)35-20(15)17)13-9-33-24(34-10-13)40-12-25(2,3)23(38)39/h5-11,31H,4,12H2,1-3H3,(H,32,35)(H,38,39)
InChIKey 
KAPAQIUVYZBYAT-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)