Ligand profile

IFM

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

Bound to: KP13_04425 — Aryl-phospho-beta-D-glucosidase bglC

Via homolog PDB 1oif UniProt Q08638 Formula C₆H₁₃NO₃
Mol. weight 147.17 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
IFM
PDB
1oif
UniProt (similar protein)
Q08638
Target protein
KP13_04425

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 147.17 Da
LogP (Crippen) -2.08
H-bond donors 4
H-bond acceptors 4
TPSA 72.72 Ų
Rotatable bonds 1
Aromatic rings 0 / 1
Heavy atoms 10
Fraction sp³ C 1.00
Formula C₆H₁₃NO₃

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 72.7
  • −1 ≤ LogP ≤ 5 -2.08
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 147.2
  • LogP ≤ 5 -2.08
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 1
  • TPSA ≤ 140 Ų 72.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C1[C@@H]([C@H]([C@@H](CN1)O)O)CO
InChI 
InChI=1S/C6H13NO3/c8-3-4-1-7-2-5(9)6(4)10/h4-10H,1-3H2/t4-,5-,6-/m1/s1
InChIKey 
QPYJXFZUIJOGNX-HSUXUTPPSA-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
PF00232

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_04425.

PDB 5

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 5

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)