Ligand profile

B46

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

Bound to: KP13_00051 — DNA gyrase subunit B

Via homolog PDB 3g7e UniProt C3SLN3 Formula C₂₁H₂₂N₆O₂S
Mol. weight 422.51 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
B46
PDB
3g7e
UniProt (similar protein)
C3SLN3
Target protein
KP13_00051

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 422.51 Da
LogP (Crippen) 3.44
H-bond donors 2
H-bond acceptors 7
TPSA 96.03 Ų
Rotatable bonds 6
Aromatic rings 3 / 4
Heavy atoms 30
Fraction sp³ C 0.33
Formula C₂₁H₂₂N₆O₂S

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 96.0
  • −1 ≤ LogP ≤ 5 3.44
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 422.5
  • LogP ≤ 5 3.44
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 7
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 96.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C#CCOC(=O)NCc1cc([nH]n1)c2c(nc(s2)c3cccnc3)N4CCCCC4
InChI 
InChI=1S/C21H22N6O2S/c1-2-11-29-21(28)23-14-16-12-17(26-25-16)18-19(27-9-4-3-5-10-27)24-20(30-18)15-7-6-8-22-13-15/h1,6-8,12-13H,3-5,9-11,14H2,(H,23,28)(H,25,26)
InChIKey 
DJDJEDRAXXHMHQ-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)