Ligand profile

12E

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

Bound to: KP13_00667 — Glycogen phosphorylase

Via homolog PDB 3mrt UniProt P00489 Formula C₁₃H₁₈N₄O₅S
Mol. weight 342.38 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
12E
PDB
3mrt
UniProt (similar protein)
P00489
Target protein
KP13_00667

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 342.38 Da
LogP (Crippen) -2.32
H-bond donors 6
H-bond acceptors 8
TPSA 139.46 Ų
Rotatable bonds 4
Aromatic rings 1 / 2
Heavy atoms 23
Fraction sp³ C 0.46
Formula C₁₃H₁₈N₄O₅S

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 139.5
  • −1 ≤ LogP ≤ 5 -2.32
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 342.4
  • LogP ≤ 5 -2.32
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 8
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 139.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cnccc1/C=N/NC(=S)N[C@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CO)O)O)O
InChI 
InChI=1S/C13H18N4O5S/c18-6-8-9(19)10(20)11(21)12(22-8)16-13(23)17-15-5-7-1-3-14-4-2-7/h1-5,8-12,18-21H,6H2,(H2,16,17,23)/b15-5+/t8-,9-,10+,11-,12-/m1/s1
InChIKey 
KHZWKRXKMLEULJ-XYUJZHSNSA-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
PF00343

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_00667.

PDB 115

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

Ligand PDB entry

ChEMBL 100

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)