Ligand profile

9JG

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

Bound to: KP13_00051 — DNA gyrase subunit B

Via homolog PDB 5mmo UniProt P0AES7 Formula C₂₂H₂₁N₅O₃
Mol. weight 403.44 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
9JG
PDB
5mmo
UniProt (similar protein)
P0AES7
Target protein
KP13_00051

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 403.44 Da
LogP (Crippen) 3.30
H-bond donors 3
H-bond acceptors 5
TPSA 105.24 Ų
Rotatable bonds 6
Aromatic rings 3 / 3
Heavy atoms 30
Fraction sp³ C 0.18
Formula C₂₂H₂₁N₅O₃

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 105.2
  • −1 ≤ LogP ≤ 5 3.30
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 403.4
  • LogP ≤ 5 3.30
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 105.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCNC(=O)Nc1cc2c(ccc(c2cn1)CNC(=O)OCC#C)c3ccncc3
InChI 
InChI=1S/C22H21N5O3/c1-3-11-30-22(29)26-13-16-5-6-17(15-7-9-23-10-8-15)18-12-20(25-14-19(16)18)27-21(28)24-4-2/h1,5-10,12,14H,4,11,13H2,2H3,(H,26,29)(H2,24,25,27,28)
InChIKey 
BRRCVBAIWLLLPK-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)