Ligand profile

ZINC3933

Virtual-screening candidate from ZINC.

Bound to: VK055_4030 — DNA topoisomerase IV, B subunit

Via homolog UniProt Q59961 Formula C₁₇H₁₇F₂N₃O₃
Tanimoto 0.81
Mol. weight 349.34 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC3933
UniProt (similar protein)
Q59961
Tanimoto
0.815
Target protein
VK055_4030

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 349.34 Da
LogP (Crippen) 1.85
H-bond donors 2
H-bond acceptors 5
TPSA 88.56 Ų
Rotatable bonds 3
Aromatic rings 2 / 4
Heavy atoms 25
Fraction sp³ C 0.41
Formula C₁₇H₁₇F₂N₃O₃

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 1.85
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 349.3
  • LogP ≤ 5 1.85
  • 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]1CCN(c2c(F)cc3c(=O)c(C(=O)O)cn(C4CC4)c3c2F)C1
InChI 
InChI=1S/C17H17F2N3O3/c18-12-5-10-14(13(19)15(12)21-4-3-8(20)6-21)22(9-1-2-9)7-11(16(10)23)17(24)25/h5,7-9H,1-4,6,20H2,(H,24,25)/t8-/m0/s1
InChIKey 
UHBXZNXCIZHGFF-QMMMGPOBSA-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)