Ligand profile

9L8

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

Bound to: KP13_00667 — Glycogen phosphorylase

Via homolog PDB 5o56 UniProt P00489 Formula C₁₈H₂₀N₄O₄
Mol. weight 356.38 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
9L8
PDB
5o56
UniProt (similar protein)
P00489
Target protein
KP13_00667

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 356.38 Da
LogP (Crippen) 0.11
H-bond donors 5
H-bond acceptors 7
TPSA 137.51 Ų
Rotatable bonds 3
Aromatic rings 3 / 4
Heavy atoms 26
Fraction sp³ C 0.33
Formula C₁₈H₂₀N₄O₄

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 137.5
  • −1 ≤ LogP ≤ 5 0.11
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 356.4
  • LogP ≤ 5 0.11
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 7
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 137.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1ccc2cc(ccc2c1)c3nc([nH]n3)[C@H]4[C@@H]([C@H]([C@@H]([C@H](O4)CO)O)O)N
InChI 
InChI=1S/C18H20N4O4/c19-13-15(25)14(24)12(8-23)26-16(13)18-20-17(21-22-18)11-6-5-9-3-1-2-4-10(9)7-11/h1-7,12-16,23-25H,8,19H2,(H,20,21,22)/t12-,13-,14-,15-,16-/m1/s1
InChIKey 
IMNCDLXOKIGZHY-OXGONZEZSA-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)