Ligand profile

57X

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

Bound to: KP13_00051 — DNA gyrase subunit B

Via homolog PDB 5d7d UniProt P0A0K8 Formula C₁₇H₁₅N₅OS
Mol. weight 337.41 Da
Permeability High
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
57X
PDB
5d7d
UniProt (similar protein)
P0A0K8
Target protein
KP13_00051

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 337.41 Da
LogP (Crippen) 3.32
H-bond donors 1
H-bond acceptors 6
TPSA 76.46 Ų
Rotatable bonds 4
Aromatic rings 4 / 4
Heavy atoms 24
Fraction sp³ C 0.18
Formula C₁₇H₁₅N₅OS

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 76.5
  • −1 ≤ LogP ≤ 5 3.32
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 337.4
  • LogP ≤ 5 3.32
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 76.5
PAINS Alert

Matches PAINS filter: dyes5A(27). May be a frequent false positive in HTS — review carefully.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCCN1c2c(c(n[nH]2)c3cnc(s3)c4cccnc4)C=CC1=O
InChI 
InChI=1S/C17H15N5OS/c1-2-8-22-14(23)6-5-12-15(20-21-16(12)22)13-10-19-17(24-13)11-4-3-7-18-9-11/h3-7,9-10H,2,8H2,1H3,(H,20,21)
InChIKey 
VOOCDNWLHBWIJZ-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)