Ligand profile

EZ6

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

Bound to: KP13_00051 — DNA gyrase subunit B

Via homolog PDB 6m1j UniProt Q9I7C2 Formula C₂₄H₁₇F₄N₇O₂
Mol. weight 511.44 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
EZ6
PDB
6m1j
UniProt (similar protein)
Q9I7C2
Target protein
KP13_00051

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 511.44 Da
LogP (Crippen) 4.67
H-bond donors 3
H-bond acceptors 7
TPSA 121.61 Ų
Rotatable bonds 5
Aromatic rings 5 / 6
Heavy atoms 37
Fraction sp³ C 0.21
Formula C₂₄H₁₇F₄N₇O₂

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 121.6
  • −1 ≤ LogP ≤ 5 4.67
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 511.4
  • LogP ≤ 5 4.67
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 7
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 121.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CNc1cc(cc2c1[nH]c3c2c(c(cn3)c4cnc(nc4)C5(CC5)C(=O)O)n6ccc(n6)C(F)(F)F)F
InChI 
InChI=1S/C24H17F4N7O2/c1-29-15-7-12(25)6-13-17-19(35-5-2-16(34-35)24(26,27)28)14(10-30-20(17)33-18(13)15)11-8-31-21(32-9-11)23(3-4-23)22(36)37/h2,5-10,29H,3-4H2,1H3,(H,30,33)(H,36,37)
InChIKey 
ANAKZQGZECWBHO-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)