Ligand profile

M09

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

Bound to: KP13_00667 — Glycogen phosphorylase

Via homolog PDB 2qrm UniProt P00489 Formula C₁₄H₁₈N₂O₈
Mol. weight 342.30 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
M09
PDB
2qrm
UniProt (similar protein)
P00489
Target protein
KP13_00667

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 342.30 Da
LogP (Crippen) -1.27
H-bond donors 5
H-bond acceptors 9
TPSA 154.55 Ų
Rotatable bonds 3
Aromatic rings 1 / 3
Heavy atoms 24
Fraction sp³ C 0.57
Formula C₁₄H₁₈N₂O₈

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 154.6
  • −1 ≤ LogP ≤ 5 -1.27
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 342.3
  • LogP ≤ 5 -1.27
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 9
Veber's rules Fail
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 154.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc(ccc1C2C[C@]3([C@@H]([C@H]([C@@H]([C@H](O3)CO)O)O)O)ON2)[N+](=O)[O-]
InChI 
InChI=1S/C14H18N2O8/c17-6-10-11(18)12(19)13(20)14(23-10)5-9(15-24-14)7-1-3-8(4-2-7)16(21)22/h1-4,9-13,15,17-20H,5-6H2/t9?,10-,11-,12+,13-,14-/m1/s1
InChIKey 
FYUHHVCQKVTVLN-MXNNCRBYSA-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)