Ligand profile

GIM

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

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

Via homolog PDB 7bzm UniProt Q75I93 Formula C₈H₁₃N₂O₄⁺
Mol. weight 201.20 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
GIM
PDB
7bzm
UniProt (similar protein)
Q75I93
Target protein
KP13_04425

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 201.20 Da
LogP (Crippen) -2.40
H-bond donors 5
H-bond acceptors 4
TPSA 100.59 Ų
Rotatable bonds 1
Aromatic rings 1 / 2
Heavy atoms 14
Fraction sp³ C 0.62
Formula C₈H₁₃N₂O₄⁺

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 100.6
  • −1 ≤ LogP ≤ 5 -2.40
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 201.2
  • LogP ≤ 5 -2.40
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 1
  • TPSA ≤ 140 Ų 100.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1c[n+]2c([nH]1)[C@@H]([C@H]([C@@H]([C@H]2CO)O)O)O
InChI 
InChI=1S/C8H12N2O4/c11-3-4-5(12)6(13)7(14)8-9-1-2-10(4)8/h1-2,4-7,11-14H,3H2/p+1/t4-,5-,6+,7-/m1/s1
InChIKey 
RZRDQZQPTISYKY-MVIOUDGNSA-O

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)