Ligand profile

XT8

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

Bound to: VK055_1865 — penicillin-binding protein 2

Via homolog PDB 6un3 UniProt G3XD46 Formula C₁₅H₁₈N₂O₆S₂
Mol. weight 386.45 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
XT8
PDB
6un3
UniProt (similar protein)
G3XD46
Target protein
VK055_1865

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 386.45 Da
LogP (Crippen) 0.49
H-bond donors 4
H-bond acceptors 7
TPSA 132.80 Ų
Rotatable bonds 7
Aromatic rings 1 / 2
Heavy atoms 25
Fraction sp³ C 0.47
Formula C₁₅H₁₈N₂O₆S₂

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 132.8
  • −1 ≤ LogP ≤ 5 0.49
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 386.5
  • LogP ≤ 5 0.49
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 7
Veber's rules Pass
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 132.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC1([C@@H](N[C@H](S1)[C@@H](C=O)NC(=O)[C@@H](c2ccsc2)C(=O)O)C(=O)O)C
InChI 
InChI=1S/C15H18N2O6S2/c1-15(2)10(14(22)23)17-12(25-15)8(5-18)16-11(19)9(13(20)21)7-3-4-24-6-7/h3-6,8-10,12,17H,1-2H3,(H,16,19)(H,20,21)(H,22,23)/t8-,9-,10+,12-/m1/s1
InChIKey 
GQZADNJRZOHJDT-MWGHHZFTSA-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
PF00905

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_1865.

PDB 24

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

Ligand PDB entry

ChEMBL 4

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)