Ligand profile

ISE

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

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

Via homolog PDB 5yaq UniProt K7ZP76 Formula C₆H₁₀O₆
Mol. weight 178.14 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ISE
PDB
5yaq
UniProt (similar protein)
K7ZP76
Target protein
KP13_03564

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 178.14 Da
LogP (Crippen) -3.63
H-bond donors 5
H-bond acceptors 6
TPSA 118.22 Ų
Rotatable bonds 0
Aromatic rings 0 / 1
Heavy atoms 12
Fraction sp³ C 0.83
Formula C₆H₁₀O₆

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 118.2
  • −1 ≤ LogP ≤ 5 -3.63
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 178.1
  • LogP ≤ 5 -3.63
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 0
  • TPSA ≤ 140 Ų 118.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
[C@H]1([C@H](C(=O)[C@H]([C@@H](C1O)O)O)O)O
InChI 
InChI=1S/C6H10O6/c7-1-2(8)4(10)6(12)5(11)3(1)9/h1-5,7-11H/t1?,2-,3+,4+,5-
InChIKey 
VYEGBDHSGHXOGT-ZLIBEWLCSA-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)