Ligand profile

948

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

Bound to: KP13_00143 — Alpha-xylosidase

Via homolog PDB 5npe UniProt B3PEE6 Formula C₇H₁₃NO₄
Mol. weight 175.18 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
948
PDB
5npe
UniProt (similar protein)
B3PEE6
Target protein
KP13_00143

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 175.18 Da
LogP (Crippen) -2.97
H-bond donors 5
H-bond acceptors 5
TPSA 102.86 Ų
Rotatable bonds 1
Aromatic rings 0 / 2
Heavy atoms 12
Fraction sp³ C 1.00
Formula C₇H₁₃NO₄

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 102.9
  • −1 ≤ LogP ≤ 5 -2.97
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 175.2
  • LogP ≤ 5 -2.97
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 1
  • TPSA ≤ 140 Ų 102.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C([C@H]1[C@@H]2[C@@H](N2)[C@@H]([C@H]([C@@H]1O)O)O)O
InChI 
InChI=1S/C7H13NO4/c9-1-2-3-4(8-3)6(11)7(12)5(2)10/h2-12H,1H2/t2-,3+,4+,5+,6-,7-/m0/s1
InChIKey 
GPIFFOGPRPKRHS-DRYVTRLFSA-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)