Ligand profile

AE8

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

Bound to: KP13_00955 — DNA gyrase subunit A

Via homolog PDB 4bul UniProt Q99XG5 Formula C₂₄H₂₆FN₅O₄
Mol. weight 467.50 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
AE8
PDB
4bul
UniProt (similar protein)
Q99XG5
Target protein
KP13_00955

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 467.50 Da
LogP (Crippen) 1.16
H-bond donors 2
H-bond acceptors 9
TPSA 101.74 Ų
Rotatable bonds 5
Aromatic rings 3 / 6
Heavy atoms 34
Fraction sp³ C 0.46
Formula C₂₄H₂₆FN₅O₄

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 101.7
  • −1 ≤ LogP ≤ 5 1.16
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 467.5
  • LogP ≤ 5 1.16
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 9
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 101.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1c(ncc2c1OCCO2)CNC3CCN(CC3)C[C@@]4(CN5c6c4c(cnc6C=CC5=O)F)O
InChI 
InChI=1S/C24H26FN5O4/c25-17-11-28-18-1-2-21(31)30-14-24(32,22(17)23(18)30)13-29-5-3-15(4-6-29)26-10-16-9-19-20(12-27-16)34-8-7-33-19/h1-2,9,11-12,15,26,32H,3-8,10,13-14H2/t24-/m0/s1
InChIKey 
VJVBZXRLYHVXIQ-DEOSSOPVSA-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_00955.

PDB 24

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ChEMBL 16

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)