Ligand profile

XYN

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

Bound to: VK055_1462 — tartrate dehydrogenase

Via homolog PDB 3asj UniProt Q5SIJ1 Formula C₅H₆O₅S
Mol. weight 178.16 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
XYN
PDB
3asj
UniProt (similar protein)
Q5SIJ1
Target protein
VK055_1462

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 178.16 Da
LogP (Crippen) -0.54
H-bond donors 2
H-bond acceptors 4
TPSA 91.67 Ų
Rotatable bonds 5
Aromatic rings 0 / 0
Heavy atoms 11
Fraction sp³ C 0.40
Formula C₅H₆O₅S

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 91.7
  • −1 ≤ LogP ≤ 5 -0.54
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 178.2
  • LogP ≤ 5 -0.54
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 91.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C(C(=O)C(=O)O)SCC(=O)O
InChI 
InChI=1S/C5H6O5S/c6-3(5(9)10)1-11-2-4(7)8/h1-2H2,(H,7,8)(H,9,10)
InChIKey 
FDUKYMHTXNDQPD-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
PF00180

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to VK055_1462.

PDB 8

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ChEMBL 1

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 10

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)