Ligand profile

4D1

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

Bound to: KP13_00667 — Glycogen phosphorylase

Via homolog PDB 4yi5 UniProt P00489 Formula C₁₉H₂₆N₂O₇
Mol. weight 394.42 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
4D1
PDB
4yi5
UniProt (similar protein)
P00489
Target protein
KP13_00667

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 394.42 Da
LogP (Crippen) -0.55
H-bond donors 6
H-bond acceptors 7
TPSA 148.35 Ų
Rotatable bonds 5
Aromatic rings 1 / 2
Heavy atoms 28
Fraction sp³ C 0.47
Formula C₁₉H₂₆N₂O₇

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 148.3
  • −1 ≤ LogP ≤ 5 -0.55
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 394.4
  • LogP ≤ 5 -0.55
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 7
Veber's rules Fail
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 148.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(C)c1ccc(cc1)/C=C/C(=O)NC(=O)N[C@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CO)O)O)O
InChI 
InChI=1S/C19H26N2O7/c1-10(2)12-6-3-11(4-7-12)5-8-14(23)20-19(27)21-18-17(26)16(25)15(24)13(9-22)28-18/h3-8,10,13,15-18,22,24-26H,9H2,1-2H3,(H2,20,21,23,27)/b8-5+/t13-,15-,16+,17-,18-/m1/s1
InChIKey 
RIYKPZZUXJMBTL-AWRGUQPNSA-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)