Ligand profile

5GF

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

Bound to: KP13_00143 — Alpha-xylosidase

Via homolog PDB 4ba0 UniProt B3PEE6 Formula C₆H₁₁FO₆
Mol. weight 198.15 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
5GF
PDB
4ba0
UniProt (similar protein)
B3PEE6
Target protein
KP13_00143

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 198.15 Da
LogP (Crippen) -2.92
H-bond donors 5
H-bond acceptors 6
TPSA 110.38 Ų
Rotatable bonds 1
Aromatic rings 0 / 1
Heavy atoms 13
Fraction sp³ C 1.00
Formula C₆H₁₁FO₆

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 -2.92
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 198.1
  • LogP ≤ 5 -2.92
  • 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 
C([C@@]1([C@H]([C@@H]([C@H]([C@@H](O1)O)O)O)O)F)O
InChI 
InChI=1S/C6H11FO6/c7-6(1-8)4(11)2(9)3(10)5(12)13-6/h2-5,8-12H,1H2/t2-,3-,4+,5-,6-/m1/s1
InChIKey 
YQZCKDSOGGIGPL-VFUOTHLCSA-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
PF01055

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_00143.

PDB 9

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

Ligand PDB entry

ChEMBL 2

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)