Ligand profile

RUG

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

Bound to: KP13_00667 — Glycogen phosphorylase

Via homolog PDB 3g2i UniProt P00489 Formula C₉H₁₅N₃O₆
Mol. weight 261.23 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
RUG
PDB
3g2i
UniProt (similar protein)
P00489
Target protein
KP13_00667

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 261.23 Da
LogP (Crippen) -3.26
H-bond donors 5
H-bond acceptors 9
TPSA 141.09 Ų
Rotatable bonds 3
Aromatic rings 1 / 2
Heavy atoms 18
Fraction sp³ C 0.78
Formula C₉H₁₅N₃O₆

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 141.1
  • −1 ≤ LogP ≤ 5 -3.26
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 261.2
  • LogP ≤ 5 -3.26
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 9
Veber's rules Fail
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 141.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1c(nnn1[C@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CO)O)O)O)CO
InChI 
InChI=1S/C9H15N3O6/c13-2-4-1-12(11-10-4)9-8(17)7(16)6(15)5(3-14)18-9/h1,5-9,13-17H,2-3H2/t5-,6-,7+,8-,9-/m1/s1
InChIKey 
BHGZOVXPACYZLI-SYHAXYEDSA-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)