Ligand profile

N1N

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

Bound to: KP13_00051 — DNA gyrase subunit B

Via homolog PDB 6tck UniProt P0A0K8 Formula C₂₁H₁₅Cl₂N₃O₄S
Mol. weight 476.34 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
N1N
PDB
6tck
UniProt (similar protein)
P0A0K8
Target protein
KP13_00051

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 476.34 Da
LogP (Crippen) 5.77
H-bond donors 3
H-bond acceptors 5
TPSA 104.31 Ų
Rotatable bonds 6
Aromatic rings 4 / 4
Heavy atoms 31
Fraction sp³ C 0.10
Formula C₂₁H₁₅Cl₂N₃O₄S

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 104.3
  • −1 ≤ LogP ≤ 5 5.77
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 476.3
  • LogP ≤ 5 5.77
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 104.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1c(c(c([nH]1)C(=O)Nc2nc3c(cc(cc3s2)C(=O)O)OCc4ccccc4)Cl)Cl
InChI 
InChI=1S/C21H15Cl2N3O4S/c1-10-15(22)16(23)18(24-10)19(27)26-21-25-17-13(30-9-11-5-3-2-4-6-11)7-12(20(28)29)8-14(17)31-21/h2-8,24H,9H2,1H3,(H,28,29)(H,25,26,27)
InChIKey 
QJJVAUMJKWWKTD-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)