Ligand profile

JK8

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

Bound to: KP13_00051 — DNA gyrase subunit B

Via homolog PDB 6qx2 UniProt P0A0K8 Formula C₂₁H₁₇ClN₂O₂
Mol. weight 364.83 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
JK8
PDB
6qx2
UniProt (similar protein)
P0A0K8
Target protein
KP13_00051

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 364.83 Da
LogP (Crippen) 5.23
H-bond donors 1
H-bond acceptors 4
TPSA 61.28 Ų
Rotatable bonds 5
Aromatic rings 4 / 4
Heavy atoms 26
Fraction sp³ C 0.10
Formula C₂₁H₁₇ClN₂O₂

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 61.3
  • −1 ≤ LogP ≤ 5 5.23
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 364.8
  • LogP ≤ 5 5.23
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 61.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1ccc(cc1)[C@H](CN)Oc2c3cc(ccc3on2)c4ccccc4Cl
InChI 
InChI=1S/C21H17ClN2O2/c22-18-9-5-4-8-16(18)15-10-11-19-17(12-15)21(24-26-19)25-20(13-23)14-6-2-1-3-7-14/h1-12,20H,13,23H2/t20-/m0/s1
InChIKey 
HHSLFPVGKCXEOG-FQEVSTJZSA-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' 'PF00986

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)