Ligand profile

ZINC2516145

Virtual-screening candidate from ZINC.

Bound to: KP13_06748 — DNA topoisomerase III

Via homolog UniProt P06612 Formula C₁₂H₁₆N₂O₆
Tanimoto 0.73
Mol. weight 284.27 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC2516145
UniProt (similar protein)
P06612
Tanimoto
0.725
Target protein
KP13_06748

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 284.27 Da
LogP (Crippen) -0.94
H-bond donors 2
H-bond acceptors 7
TPSA 110.62 Ų
Rotatable bonds 3
Aromatic rings 1 / 2
Heavy atoms 20
Fraction sp³ C 0.58
Formula C₁₂H₁₆N₂O₆

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 110.6
  • −1 ≤ LogP ≤ 5 -0.94
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 284.3
  • LogP ≤ 5 -0.94
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 7
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 110.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(=O)O[C@@H]1C[C@@H](n2cc(C)c(=O)[nH]c2=O)O[C@H]1CO
InChI 
InChI=1S/C12H16N2O6/c1-6-4-14(12(18)13-11(6)17)10-3-8(19-7(2)16)9(5-15)20-10/h4,8-10,15H,3,5H2,1-2H3,(H,13,17,18)/t8-,9+,10+/m1/s1
InChIKey 
IRFKBRPHBYCMQU-UTLUCORTSA-N

Provenance

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

Method
LigQ nearest_k
Query
T3P
Homolog
P06612

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_06748.

PDB 3

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

Ligand PDB entry

ZINC 49

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)