Ligand profile

AF5

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

Bound to: VK055_4030 — DNA topoisomerase IV, B subunit

Via homolog PDB 4kpe UniProt Q59961 Formula C₂₀H₂₀FN₃O₃
Mol. weight 369.40 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
AF5
PDB
4kpe
UniProt (similar protein)
Q59961
Target protein
VK055_4030

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 369.40 Da
LogP (Crippen) 2.50
H-bond donors 2
H-bond acceptors 5
TPSA 88.56 Ų
Rotatable bonds 2
Aromatic rings 2 / 5
Heavy atoms 27
Fraction sp³ C 0.40
Formula C₂₀H₂₀FN₃O₃

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 88.6
  • −1 ≤ LogP ≤ 5 2.50
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 369.4
  • LogP ≤ 5 2.50
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 88.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1c2c(c3c(c1F)N4CC[C@H]([C@H]4CC=C3)N)N(C=C(C2=O)C(=O)O)C5CC5
InChI 
InChI=1S/C20H20FN3O3/c21-14-8-12-17(24(10-4-5-10)9-13(19(12)25)20(26)27)11-2-1-3-16-15(22)6-7-23(16)18(11)14/h1-2,8-10,15-16H,3-7,22H2,(H,26,27)/t15-,16-/m1/s1
InChIKey 
KZNQXATUOHSRHR-HZPDHXFCSA-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 VK055_4030.

PDB 19

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

Ligand PDB entry

ChEMBL 18

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)