Ligand profile

DU5

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

Bound to: KP13_00051 — DNA gyrase subunit B

Via homolog PDB 6fm4 UniProt P66937 Formula C₂₃H₂₆N₄O
Mol. weight 374.49 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
DU5
PDB
6fm4
UniProt (similar protein)
P66937
Target protein
KP13_00051

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 374.49 Da
LogP (Crippen) 3.18
H-bond donors 1
H-bond acceptors 4
TPSA 48.47 Ų
Rotatable bonds 6
Aromatic rings 3 / 4
Heavy atoms 28
Fraction sp³ C 0.30
Formula C₂₃H₂₆N₄O

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy High

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 48.5
  • −1 ≤ LogP ≤ 5 3.18
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 374.5
  • LogP ≤ 5 3.18
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 48.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1ccc(cc1)C(=O)NCCCN2CCN(CC2)c3c4ccccc4ccn3
InChI 
InChI=1S/C23H26N4O/c28-23(20-8-2-1-3-9-20)25-12-6-14-26-15-17-27(18-16-26)22-21-10-5-4-7-19(21)11-13-24-22/h1-5,7-11,13H,6,12,14-18H2,(H,25,28)
InChIKey 
FJTUELRAUXXLBI-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
PF00521

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)