Ligand profile

1YP

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

Bound to: VK055_4030 — DNA topoisomerase IV, B subunit

Via homolog PDB 4lpb UniProt Q8DQB5 Formula C₁₉H₁₄F₃N₇O₃S
Mol. weight 477.43 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
1YP
PDB
4lpb
UniProt (similar protein)
Q8DQB5
Target protein
VK055_4030

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 477.43 Da
LogP (Crippen) 3.77
H-bond donors 3
H-bond acceptors 8
TPSA 138.69 Ų
Rotatable bonds 5
Aromatic rings 4 / 4
Heavy atoms 33
Fraction sp³ C 0.16
Formula C₁₉H₁₄F₃N₇O₃S

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 138.7
  • −1 ≤ LogP ≤ 5 3.77
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 477.4
  • LogP ≤ 5 3.77
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 8
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 138.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCNC(=O)Nc1cc(c(cn1)c2cc(cnc2)C3=NNC(=O)O3)c4nc(cs4)C(F)(F)F
InChI 
InChI=1S/C19H14F3N7O3S/c1-2-24-17(30)27-14-4-11(16-26-13(8-33-16)19(20,21)22)12(7-25-14)9-3-10(6-23-5-9)15-28-29-18(31)32-15/h3-8H,2H2,1H3,(H,29,31)(H2,24,25,27,30)
InChIKey 
VIHKUWHFUWMXKJ-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)