Ligand profile

D0K

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

Bound to: KP13_00051 — DNA gyrase subunit B

Via homolog PDB 6f96 UniProt P0AES6 Formula C₂₁H₂₂N₆O₃
Mol. weight 406.45 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
D0K
PDB
6f96
UniProt (similar protein)
P0AES6
Target protein
KP13_00051

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 406.45 Da
LogP (Crippen) 3.62
H-bond donors 4
H-bond acceptors 6
TPSA 117.27 Ų
Rotatable bonds 7
Aromatic rings 3 / 3
Heavy atoms 30
Fraction sp³ C 0.14
Formula C₂₁H₂₂N₆O₃

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 117.3
  • −1 ≤ LogP ≤ 5 3.62
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 406.4
  • LogP ≤ 5 3.62
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 117.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCNC(=O)Nc1cc(c(cn1)C(=O)Nc2cccnc2)Nc3ccc(cc3)OC
InChI 
InChI=1S/C21H22N6O3/c1-3-23-21(29)27-19-11-18(25-14-6-8-16(30-2)9-7-14)17(13-24-19)20(28)26-15-5-4-10-22-12-15/h4-13H,3H2,1-2H3,(H,26,28)(H3,23,24,25,27,29)
InChIKey 
FSOAZMGZMXDGQX-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)