Ligand profile

1AV

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

Bound to: VK055_4030 — DNA topoisomerase IV, B subunit

Via homolog PDB 4hz0 UniProt P20083 Formula C₁₃H₉N₇S
Mol. weight 295.33 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
1AV
PDB
4hz0
UniProt (similar protein)
P20083
Target protein
VK055_4030

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 295.33 Da
LogP (Crippen) 1.92
H-bond donors 1
H-bond acceptors 8
TPSA 95.40 Ų
Rotatable bonds 2
Aromatic rings 4 / 4
Heavy atoms 21
Fraction sp³ C 0.00
Formula C₁₃H₉N₇S

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 95.4
  • −1 ≤ LogP ≤ 5 1.92
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 295.3
  • LogP ≤ 5 1.92
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 8
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 95.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc(cnc1)c2nc3c(nc(nc3s2)N)n4ccnc4
InChI 
InChI=1S/C13H9N7S/c14-13-18-10(20-5-4-16-7-20)9-12(19-13)21-11(17-9)8-2-1-3-15-6-8/h1-7H,(H2,14,18,19)
InChIKey 
FTDVRDNCBWDKFI-UHFFFAOYSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ sequence
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)