Ligand profile

SOE

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

Bound to: KP13_03564 — Gfo/Idh/MocA family oxidoreductase

Via homolog PDB 6a3j UniProt F0M433 Formula C₆H₁₂O₆
Mol. weight 180.16 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
SOE
PDB
6a3j
UniProt (similar protein)
F0M433
Target protein
KP13_03564

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 180.16 Da
LogP (Crippen) -3.22
H-bond donors 5
H-bond acceptors 6
TPSA 110.38 Ų
Rotatable bonds 1
Aromatic rings 0 / 1
Heavy atoms 12
Fraction sp³ C 1.00
Formula C₆H₁₂O₆

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 110.4
  • −1 ≤ LogP ≤ 5 -3.22
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 180.2
  • LogP ≤ 5 -3.22
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 1
  • TPSA ≤ 140 Ų 110.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C1[C@@H]([C@H]([C@@H]([C@](O1)(CO)O)O)O)O
InChI 
InChI=1S/C6H12O6/c7-2-6(11)5(10)4(9)3(8)1-12-6/h3-5,7-11H,1-2H2/t3-,4+,5-,6+/m0/s1
InChIKey 
LKDRXBCSQODPBY-BGPJRJDNSA-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
PF01408' 'PF22725

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_03564.

PDB 8

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)