Ligand profile

ZINC1529898

Virtual-screening candidate from ZINC.

Bound to: KP13_02784 — DNA topoisomerase 4 subunit A

Via homolog UniProt Q99XG5 Formula C₉H₁₂FN₂O₈P
Tanimoto 0.78
Mol. weight 326.17 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC1529898
UniProt (similar protein)
Q99XG5
Tanimoto
0.776
Target protein
KP13_02784

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 326.17 Da
LogP (Crippen) -1.57
H-bond donors 4
H-bond acceptors 7
TPSA 151.08 Ų
Rotatable bonds 4
Aromatic rings 1 / 2
Heavy atoms 21
Fraction sp³ C 0.56
Formula C₉H₁₂FN₂O₈P

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 151.1
  • −1 ≤ LogP ≤ 5 -1.57
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 326.2
  • LogP ≤ 5 -1.57
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 7
Veber's rules Fail
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 151.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
O=c1[nH]c(=O)n([C@@H]2C[C@@H](O)[C@H](COP(=O)(O)O)O2)cc1F
InChI 
InChI=1S/C9H12FN2O8P/c10-4-2-12(9(15)11-8(4)14)7-1-5(13)6(20-7)3-19-21(16,17)18/h2,5-7,13H,1,3H2,(H,11,14,15)(H2,16,17,18)/t5-,6+,7+/m1/s1
InChIKey 
HFEKDTCAMMOLQP-VQVTYTSYSA-N

Provenance

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

Method
LigQ nearest_k
Query
DT
Homolog
Q99XG5

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)