Ligand profile

ON2

Ligand co-crystallized with a similar protein (Protein Data Bank).

Bound to: KP13_00051 — DNA gyrase subunit B

Via homolog PDB 6yd9 UniProt P0AES6 Formula C₁₆H₁₅Cl₂N₅O₂S
Mol. weight 412.30 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ON2
PDB
6yd9
UniProt (similar protein)
P0AES6
Target protein
KP13_00051

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 412.30 Da
LogP (Crippen) 3.78
H-bond donors 4
H-bond acceptors 5
TPSA 112.90 Ų
Rotatable bonds 5
Aromatic rings 3 / 3
Heavy atoms 26
Fraction sp³ C 0.19
Formula C₁₆H₁₅Cl₂N₅O₂S

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 112.9
  • −1 ≤ LogP ≤ 5 3.78
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 412.3
  • LogP ≤ 5 3.78
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 112.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1c(c(c([nH]1)C(=O)Nc2nc3ccc(cc3s2)NC(=O)CCN)Cl)Cl
InChI 
InChI=1S/C16H15Cl2N5O2S/c1-7-12(17)13(18)14(20-7)15(25)23-16-22-9-3-2-8(6-10(9)26-16)21-11(24)4-5-19/h2-3,6,20H,4-5,19H2,1H3,(H,21,24)(H,22,23,25)
InChIKey 
RVKKBUSSKLNKTC-UHFFFAOYSA-N

Provenance

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

Method
LigQ sequence
Source
PDB
Binding sites
PF02518

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_00051.

PDB 87

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

Ligand PDB entry

ChEMBL 100

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 50

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

Compound Similarity (Tanimoto)