Ligand profile

O54

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

Bound to: KP13_00051 — DNA gyrase subunit B

Via homolog PDB 5mmn UniProt P0AES7 Formula C₁₉H₂₀N₄O
Mol. weight 320.40 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
O54
PDB
5mmn
UniProt (similar protein)
P0AES7
Target protein
KP13_00051

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 320.40 Da
LogP (Crippen) 4.06
H-bond donors 2
H-bond acceptors 3
TPSA 66.91 Ų
Rotatable bonds 3
Aromatic rings 3 / 3
Heavy atoms 24
Fraction sp³ C 0.21
Formula C₁₉H₂₀N₄O

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 66.9
  • −1 ≤ LogP ≤ 5 4.06
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 320.4
  • LogP ≤ 5 4.06
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 66.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCNC(=O)Nc1cc2c(ccc(c2cn1)C)c3ccnc(c3)C
InChI 
InChI=1S/C19H20N4O/c1-4-20-19(24)23-18-10-16-15(14-7-8-21-13(3)9-14)6-5-12(2)17(16)11-22-18/h5-11H,4H2,1-3H3,(H2,20,22,23,24)
InChIKey 
ITGDBTWKMCUOIO-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)