Ligand profile

57U

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

Bound to: KP13_00051 — DNA gyrase subunit B

Via homolog PDB 5d6p UniProt P0A0K8 Formula C₁₁H₁₄N₄O₂S
Mol. weight 266.33 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
57U
PDB
5d6p
UniProt (similar protein)
P0A0K8
Target protein
KP13_00051

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 266.33 Da
LogP (Crippen) 1.77
H-bond donors 4
H-bond acceptors 4
TPSA 90.04 Ų
Rotatable bonds 4
Aromatic rings 2 / 2
Heavy atoms 18
Fraction sp³ C 0.27
Formula C₁₁H₁₄N₄O₂S

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 90.0
  • −1 ≤ LogP ≤ 5 1.77
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 266.3
  • LogP ≤ 5 1.77
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 90.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCNC(=O)Nc1nc(c(s1)c2ccc[nH]2)CO
InChI 
InChI=1S/C11H14N4O2S/c1-2-12-10(17)15-11-14-8(6-16)9(18-11)7-4-3-5-13-7/h3-5,13,16H,2,6H2,1H3,(H2,12,14,15,17)
InChIKey 
YLSYQKDIZQYYGN-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)