Ligand profile

6EJ

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

Bound to: KP13_00051 — DNA gyrase subunit B

Via homolog PDB 5npp UniProt P66937 Formula C₂₄H₂₆FN₅O₃
Mol. weight 451.50 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
6EJ
PDB
5npp
UniProt (similar protein)
P66937
Target protein
KP13_00051

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 451.50 Da
LogP (Crippen) 2.05
H-bond donors 1
H-bond acceptors 8
TPSA 81.51 Ų
Rotatable bonds 5
Aromatic rings 3 / 6
Heavy atoms 33
Fraction sp³ C 0.46
Formula C₂₄H₂₆FN₅O₃

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 81.5
  • −1 ≤ LogP ≤ 5 2.05
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 451.5
  • LogP ≤ 5 2.05
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 8
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 81.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc(c2c3c1C=CC(=O)N3C[C@H]2CN4CCC(CC4)NCc5cc6c(nn5)OCCO6)F
InChI 
InChI=1S/C24H26FN5O3/c25-19-3-1-15-2-4-21(31)30-14-16(22(19)23(15)30)13-29-7-5-17(6-8-29)26-12-18-11-20-24(28-27-18)33-10-9-32-20/h1-4,11,16-17,26H,5-10,12-14H2/t16-/m1/s1
InChIKey 
SRICOHRDRMZREQ-MRXNPFEDSA-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

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)