Ligand profile

TSJ

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

Bound to: VK055_4030 — DNA topoisomerase IV, B subunit

Via homolog PDB 5boc UniProt Q8DQB5 Formula C₂₀H₁₆F₃N₃O₃
Mol. weight 403.36 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
TSJ
PDB
5boc
UniProt (similar protein)
Q8DQB5
Target protein
VK055_4030

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 403.36 Da
LogP (Crippen) 4.66
H-bond donors 3
H-bond acceptors 3
TPSA 95.08 Ų
Rotatable bonds 4
Aromatic rings 3 / 3
Heavy atoms 29
Fraction sp³ C 0.15
Formula C₂₀H₁₆F₃N₃O₃

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 95.1
  • −1 ≤ LogP ≤ 5 4.66
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 403.4
  • LogP ≤ 5 4.66
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 95.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1cc(cc(c1)C(F)(F)F)c2cc([nH]n2)NC(=O)c3ccc(cc3C)C(=O)O
InChI 
InChI=1S/C20H16F3N3O3/c1-10-5-13(8-14(6-10)20(21,22)23)16-9-17(26-25-16)24-18(27)15-4-3-12(19(28)29)7-11(15)2/h3-9H,1-2H3,(H,28,29)(H2,24,25,26,27)
InChIKey 
MLGFDWKUOYDRDY-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 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)