Ligand profile

AM3

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

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

Via homolog PDB 2wc3 UniProt Q08638 Formula C₁₅H₂₈N₂O₅
Mol. weight 316.40 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
AM3
PDB
2wc3
UniProt (similar protein)
Q08638
Target protein
KP13_04425

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 316.40 Da
LogP (Crippen) -0.18
H-bond donors 4
H-bond acceptors 6
TPSA 105.75 Ų
Rotatable bonds 7
Aromatic rings 0 / 2
Heavy atoms 22
Fraction sp³ C 0.93
Formula C₁₅H₂₈N₂O₅

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 105.8
  • −1 ≤ LogP ≤ 5 -0.18
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 316.4
  • LogP ≤ 5 -0.18
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 105.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCCCCCCC/N=C\1/N2[C@H](CO1)[C@@H]([C@@H]([C@H]([C@@H]2O)O)O)O
InChI 
InChI=1S/C15H28N2O5/c1-2-3-4-5-6-7-8-16-15-17-10(9-22-15)11(18)12(19)13(20)14(17)21/h10-14,18-21H,2-9H2,1H3/b16-15-/t10-,11+,12+,13-,14+/m1/s1
InChIKey 
QJILQIWQVOAQBB-FOERHGQSSA-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)