Ligand profile

07N

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

Bound to: KP13_00051 — DNA gyrase subunit B

Via homolog PDB 3ttz UniProt P0A0K8 Formula C₁₅H₁₅Cl₂FN₄O₃S
Mol. weight 421.28 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
07N
PDB
3ttz
UniProt (similar protein)
P0A0K8
Target protein
KP13_00051

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 421.28 Da
LogP (Crippen) 3.13
H-bond donors 3
H-bond acceptors 5
TPSA 98.32 Ų
Rotatable bonds 4
Aromatic rings 2 / 3
Heavy atoms 26
Fraction sp³ C 0.40
Formula C₁₅H₁₅Cl₂FN₄O₃S

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 98.3
  • −1 ≤ LogP ≤ 5 3.13
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 421.3
  • LogP ≤ 5 3.13
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 98.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1c(c(c([nH]1)C(=O)N[C@@H]2CCN(C[C@@H]2F)c3ncc(s3)C(=O)O)Cl)Cl
InChI 
InChI=1S/C15H15Cl2FN4O3S/c1-6-10(16)11(17)12(20-6)13(23)21-8-2-3-22(5-7(8)18)15-19-4-9(26-15)14(24)25/h4,7-8,20H,2-3,5H2,1H3,(H,21,23)(H,24,25)/t7-,8+/m0/s1
InChIKey 
BGDGHNSKANYMHF-JGVFFNPUSA-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)