Ligand profile

PXN

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

Bound to: VK055_3750 — translation elongation factor Tu

Via homolog PDB 3mmp UniProt P0CE48 Formula C₁₇H₃₆O₈
Mol. weight 368.47 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
PXN
PDB
3mmp
UniProt (similar protein)
P0CE48
Target protein
VK055_3750

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 368.47 Da
LogP (Crippen) -0.44
H-bond donors 4
H-bond acceptors 8
TPSA 117.84 Ų
Rotatable bonds 16
Aromatic rings 0 / 0
Heavy atoms 25
Fraction sp³ C 1.00
Formula C₁₇H₃₆O₈

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 117.8
  • −1 ≤ LogP ≤ 5 -0.44
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 368.5
  • LogP ≤ 5 -0.44
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 8
Veber's rules Fail
  • Rotatable bonds ≤ 10 16
  • TPSA ≤ 140 Ų 117.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@H](COCC(COC[C@@H](C)O)(COC[C@@H](C)O)COC[C@H](C)O)O
InChI 
InChI=1S/C17H36O8/c1-13(18)5-22-9-17(10-23-6-14(2)19,11-24-7-15(3)20)12-25-8-16(4)21/h13-16,18-21H,5-12H2,1-4H3/t13-,14-,15-,16+/m1/s1
InChIKey 
GXEZGLLPFFKHGE-FPCVCCKLSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ sequence
Source
PDB
Binding sites
PF03144' 'PF03431

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_3750.

PDB 19

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

Ligand PDB entry

ZINC 50

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

Compound Similarity (Tanimoto)