Ligand profile

19Y

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

Bound to: VK055_4030 — DNA topoisomerase IV, B subunit

Via homolog PDB 4hxz UniProt A0A0J9WZF0 Formula C₁₅H₁₄N₄O₂S
Mol. weight 314.37 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
19Y
PDB
4hxz
UniProt (similar protein)
A0A0J9WZF0
Target protein
VK055_4030

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 314.37 Da
LogP (Crippen) 2.89
H-bond donors 1
H-bond acceptors 6
TPSA 80.76 Ų
Rotatable bonds 5
Aromatic rings 3 / 3
Heavy atoms 22
Fraction sp³ C 0.20
Formula C₁₅H₁₄N₄O₂S

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 80.8
  • −1 ≤ LogP ≤ 5 2.89
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 314.4
  • LogP ≤ 5 2.89
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 80.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCc1c(c2c([nH]1)nc(nc2OC)Sc3cccnc3)C=O
InChI 
InChI=1S/C15H14N4O2S/c1-3-11-10(8-20)12-13(17-11)18-15(19-14(12)21-2)22-9-5-4-6-16-7-9/h4-8H,3H2,1-2H3,(H,17,18,19)
InChIKey 
LEMXQPJEGCAOFY-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)