Ligand profile

08B

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

Bound to: KP13_00051 — DNA gyrase subunit B

Via homolog PDB 3u2d UniProt P0A0K8 Formula C₁₆H₁₈BrN₅O₃
Mol. weight 408.26 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
08B
PDB
3u2d
UniProt (similar protein)
P0A0K8
Target protein
KP13_00051

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 408.26 Da
LogP (Crippen) 2.79
H-bond donors 2
H-bond acceptors 5
TPSA 104.16 Ų
Rotatable bonds 4
Aromatic rings 2 / 3
Heavy atoms 25
Fraction sp³ C 0.38
Formula C₁₆H₁₈BrN₅O₃

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 104.2
  • −1 ≤ LogP ≤ 5 2.79
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 408.3
  • LogP ≤ 5 2.79
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 104.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1c(cc([nH]1)C(=O)NC2CCN(CC2)c3c(cccn3)[N+](=O)[O-])Br
InChI 
InChI=1S/C16H18BrN5O3/c1-10-12(17)9-13(19-10)16(23)20-11-4-7-21(8-5-11)15-14(22(24)25)3-2-6-18-15/h2-3,6,9,11,19H,4-5,7-8H2,1H3,(H,20,23)
InChIKey 
AUXATGQLTJKTRN-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)