Ligand profile

ZINC5932777

Virtual-screening candidate from ZINC.

Bound to: KP13_02784 — DNA topoisomerase 4 subunit A

Via homolog UniProt B0VP98 Formula C₂₀H₂₁F₂N₃O₃
Tanimoto 0.84
Mol. weight 389.40 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC5932777
UniProt (similar protein)
B0VP98
Tanimoto
0.839
Target protein
KP13_02784

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 389.40 Da
LogP (Crippen) 2.50
H-bond donors 2
H-bond acceptors 5
TPSA 74.57 Ų
Rotatable bonds 3
Aromatic rings 2 / 5
Heavy atoms 28
Fraction sp³ C 0.50
Formula C₂₀H₂₁F₂N₃O₃

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 74.6
  • −1 ≤ LogP ≤ 5 2.50
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 389.4
  • LogP ≤ 5 2.50
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 74.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
O=C(O)c1cn(C2CC2)c2c(F)c(N3C[C@@H]4CCCN[C@@H]4C3)c(F)cc2c1=O
InChI 
InChI=1S/C20H21F2N3O3/c21-14-6-12-17(25(11-3-4-11)8-13(19(12)26)20(27)28)16(22)18(14)24-7-10-2-1-5-23-15(10)9-24/h6,8,10-11,15,23H,1-5,7,9H2,(H,27,28)/t10-,15+/m0/s1
InChIKey 
WEXQOLCYKFJAJZ-ZUZCIYMTSA-N

Provenance

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

Method
LigQ nearest_k
Query
MFX
Homolog
B0VP98

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to KP13_02784.

PDB 23

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ChEMBL 15

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)