Ligand profile

ZINC3826253

Virtual-screening candidate from ZINC.

Bound to: KP13_02784 — DNA topoisomerase 4 subunit A

Via homolog UniProt B0VP98 Formula C₂₁H₂₄FN₃O₄
Tanimoto 1.00
Mol. weight 401.44 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC3826253
UniProt (similar protein)
B0VP98
Tanimoto
1.000
Target protein
KP13_02784

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 401.44 Da
LogP (Crippen) 2.37
H-bond donors 2
H-bond acceptors 6
TPSA 83.80 Ų
Rotatable bonds 4
Aromatic rings 2 / 5
Heavy atoms 29
Fraction sp³ C 0.52
Formula C₂₁H₂₄FN₃O₄

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 83.8
  • −1 ≤ LogP ≤ 5 2.37
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 401.4
  • LogP ≤ 5 2.37
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 83.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
COc1c(N2C[C@@H]3CCCN[C@@H]3C2)c(F)cc2c(=O)c(C(=O)O)cn(C3CC3)c12
InChI 
InChI=1S/C21H24FN3O4/c1-29-20-17-13(19(26)14(21(27)28)9-25(17)12-4-5-12)7-15(22)18(20)24-8-11-3-2-6-23-16(11)10-24/h7,9,11-12,16,23H,2-6,8,10H2,1H3,(H,27,28)/t11-,16+/m0/s1
InChIKey 
FABPRXSRWADJSP-MEDUHNTESA-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)