Ligand profile

ZINC3787097

Virtual-screening candidate from ZINC.

Bound to: VK055_4030 — DNA topoisomerase IV, B subunit

Via homolog UniProt Q59961 Formula C₁₉H₂₁ClFN₃O₃
Tanimoto 0.87
Mol. weight 393.85 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC3787097
UniProt (similar protein)
Q59961
Tanimoto
0.873
Target protein
VK055_4030

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 393.85 Da
LogP (Crippen) 3.14
H-bond donors 2
H-bond acceptors 5
TPSA 88.56 Ų
Rotatable bonds 3
Aromatic rings 2 / 4
Heavy atoms 27
Fraction sp³ C 0.47
Formula C₁₉H₂₁ClFN₃O₃

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 3.14
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 393.8
  • LogP ≤ 5 3.14
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 88.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
N[C@@H]1CCCCN(c2c(F)cc3c(=O)c(C(=O)O)cn(C4CC4)c3c2Cl)C1
InChI 
InChI=1S/C19H21ClFN3O3/c20-15-16-12(18(25)13(19(26)27)9-24(16)11-4-5-11)7-14(21)17(15)23-6-2-1-3-10(22)8-23/h7,9-11H,1-6,8,22H2,(H,26,27)/t10-/m1/s1
InChIKey 
QFFGVLORLPOAEC-SNVBAGLBSA-N

Provenance

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

Method
LigQ nearest_k
Query
NFX
Homolog
Q59961

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 20

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 49

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)