Ligand profile

KDG

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

Bound to: KP13_00058 — D-galactonate dehydratase

Via homolog PDB 3p93 UniProt Q1QT89 Formula C₆H₁₀O₆
Mol. weight 178.14 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
KDG
PDB
3p93
UniProt (similar protein)
Q1QT89
Target protein
KP13_00058

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 178.14 Da
LogP (Crippen) -2.26
H-bond donors 4
H-bond acceptors 5
TPSA 115.06 Ų
Rotatable bonds 5
Aromatic rings 0 / 0
Heavy atoms 12
Fraction sp³ C 0.67
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 115.1
  • −1 ≤ LogP ≤ 5 -2.26
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 178.1
  • LogP ≤ 5 -2.26
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 115.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C([C@@H]([C@@H](CO)O)O)C(=O)C(=O)O
InChI 
InChI=1S/C6H10O6/c7-2-5(10)3(8)1-4(9)6(11)12/h3,5,7-8,10H,1-2H2,(H,11,12)/t3-,5+/m0/s1
InChIKey 
WPAMZTWLKIDIOP-WVZVXSGGSA-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
PF02746' 'PF13378

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_00058.

PDB 6

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)