Ligand profile

B47

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

Bound to: KP13_00051 — DNA gyrase subunit B

Via homolog PDB 3g7b UniProt P0A0K8 Formula C₂₀H₂₃N₅O₃S
Mol. weight 413.50 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
B47
PDB
3g7b
UniProt (similar protein)
P0A0K8
Target protein
KP13_00051

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 413.50 Da
LogP (Crippen) 3.02
H-bond donors 3
H-bond acceptors 7
TPSA 103.37 Ų
Rotatable bonds 5
Aromatic rings 3 / 4
Heavy atoms 29
Fraction sp³ C 0.35
Formula C₂₀H₂₃N₅O₃S

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 103.4
  • −1 ≤ LogP ≤ 5 3.02
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 413.5
  • LogP ≤ 5 3.02
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 7
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 103.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
COC(=O)NCc1cc([nH]n1)c2c(nc(s2)c3ccccc3)N4CCC(CC4)O
InChI 
InChI=1S/C20H23N5O3S/c1-28-20(27)21-12-14-11-16(24-23-14)17-18(25-9-7-15(26)8-10-25)22-19(29-17)13-5-3-2-4-6-13/h2-6,11,15,26H,7-10,12H2,1H3,(H,21,27)(H,23,24)
InChIKey 
GFUMDRBVYNGSBP-UHFFFAOYSA-N

Provenance

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

Method
LigQ nearest_k
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)