Ligand profile

57W

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

Bound to: KP13_00051 — DNA gyrase subunit B

Via homolog PDB 5d7c UniProt P0A0K8 Formula C₂₀H₁₈N₆O
Mol. weight 358.41 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
57W
PDB
5d7c
UniProt (similar protein)
P0A0K8
Target protein
KP13_00051

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 358.41 Da
LogP (Crippen) 3.62
H-bond donors 2
H-bond acceptors 5
TPSA 84.73 Ų
Rotatable bonds 4
Aromatic rings 4 / 4
Heavy atoms 27
Fraction sp³ C 0.10
Formula C₂₀H₁₈N₆O

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 84.7
  • −1 ≤ LogP ≤ 5 3.62
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 358.4
  • LogP ≤ 5 3.62
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 84.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCNC(=O)Nc1cn(c2c1ncc(c2)c3cccnc3)c4ccccn4
InChI 
InChI=1S/C20H18N6O/c1-2-22-20(27)25-16-13-26(18-7-3-4-9-23-18)17-10-15(12-24-19(16)17)14-6-5-8-21-11-14/h3-13H,2H2,1H3,(H2,22,25,27)
InChIKey 
FRDSIJNIQUPVHU-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)