Ligand profile

57Y

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

Bound to: KP13_00051 — DNA gyrase subunit B

Via homolog PDB 5d7r UniProt P0A0K8 Formula C₁₉H₁₆N₄O₄S
Mol. weight 396.43 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
57Y
PDB
5d7r
UniProt (similar protein)
P0A0K8
Target protein
KP13_00051

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 396.43 Da
LogP (Crippen) 3.81
H-bond donors 4
H-bond acceptors 7
TPSA 132.22 Ų
Rotatable bonds 5
Aromatic rings 4 / 4
Heavy atoms 28
Fraction sp³ C 0.16
Formula C₁₉H₁₆N₄O₄S

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 132.2
  • −1 ≤ LogP ≤ 5 3.81
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 396.4
  • LogP ≤ 5 3.81
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 7
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 132.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCCc1c(ccc2c1n[nH]c2c3cnc(s3)c4cc(c(nc4)C(=O)O)O)O
InChI 
InChI=1S/C19H16N4O4S/c1-2-3-10-12(24)5-4-11-15(10)22-23-16(11)14-8-21-18(28-14)9-6-13(25)17(19(26)27)20-7-9/h4-8,24-25H,2-3H2,1H3,(H,22,23)(H,26,27)
InChIKey 
YZWBQSFGTLQFTB-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)