Ligand profile

PE8

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

Bound to: KP13_02726 — S-adenosylmethionine synthase

Via homolog PDB 6vd1 UniProt P17562 Formula C₁₆H₃₄O₉
Mol. weight 370.44 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
PE8
PDB
6vd1
UniProt (similar protein)
P17562
Target protein
KP13_02726

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 370.44 Da
LogP (Crippen) -0.91
H-bond donors 2
H-bond acceptors 9
TPSA 105.07 Ų
Rotatable bonds 22
Aromatic rings 0 / 0
Heavy atoms 25
Fraction sp³ C 1.00
Formula C₁₆H₃₄O₉

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 105.1
  • −1 ≤ LogP ≤ 5 -0.91
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 370.4
  • LogP ≤ 5 -0.91
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 9
Veber's rules Fail
  • Rotatable bonds ≤ 10 22
  • TPSA ≤ 140 Ų 105.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C(COCCOCCOCCOCCOCCOCCOCCO)O
InChI 
InChI=1S/C16H34O9/c17-1-3-19-5-7-21-9-11-23-13-15-25-16-14-24-12-10-22-8-6-20-4-2-18/h17-18H,1-16H2
InChIKey 
GLZWNFNQMJAZGY-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
PF00438' 'PF02772' 'PF02773

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_02726.

PDB 19

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)