Ligand profile

ZINC255979447

Virtual-screening candidate from ZINC.

Bound to: KP13_02784 — DNA topoisomerase 4 subunit A

Via homolog UniProt B0VP98 Formula C₂₀H₂₂FN₃O₄
Tanimoto 0.80
Mol. weight 387.41 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC255979447
UniProt (similar protein)
B0VP98
Tanimoto
0.797
Target protein
KP13_02784

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 387.41 Da
LogP (Crippen) 2.07
H-bond donors 3
H-bond acceptors 6
TPSA 94.80 Ų
Rotatable bonds 3
Aromatic rings 2 / 5
Heavy atoms 28
Fraction sp³ C 0.50
Formula C₂₀H₂₂FN₃O₄

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 94.8
  • −1 ≤ LogP ≤ 5 2.07
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 387.4
  • LogP ≤ 5 2.07
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 94.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
O=C(O)c1cn(C2CC2)c2c(O)c(N3C[C@@H]4CCCN[C@H]4C3)c(F)cc2c1=O
InChI 
InChI=1S/C20H22FN3O4/c21-14-6-12-16(24(11-3-4-11)8-13(18(12)25)20(27)28)19(26)17(14)23-7-10-2-1-5-22-15(10)9-23/h6,8,10-11,15,22,26H,1-5,7,9H2,(H,27,28)/t10-,15-/m0/s1
InChIKey 
IRASTQSQRDRSEH-BONVTDFDSA-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)