Ligand profile

HX3

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

Bound to: KP13_00051 — DNA gyrase subunit B

Via homolog PDB 5z9b UniProt P0AES6 Formula C₆H₆Cl₂N₂
Mol. weight 177.03 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
HX3
PDB
5z9b
UniProt (similar protein)
P0AES6
Target protein
KP13_00051

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 177.03 Da
LogP (Crippen) 2.28
H-bond donors 2
H-bond acceptors 2
TPSA 38.05 Ų
Rotatable bonds 1
Aromatic rings 1 / 1
Heavy atoms 10
Fraction sp³ C 0.00
Formula C₆H₆Cl₂N₂

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 38.0
  • −1 ≤ LogP ≤ 5 2.28
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 177.0
  • LogP ≤ 5 2.28
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 2
Veber's rules Pass
  • Rotatable bonds ≤ 10 1
  • TPSA ≤ 140 Ų 38.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc(c(cc1NN)Cl)Cl
InChI 
InChI=1S/C6H6Cl2N2/c7-5-2-1-4(10-9)3-6(5)8/h1-3,10H,9H2
InChIKey 
YMJSQPNVQRHZDW-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)