MolNFT v1 · #170508 · protein
Crystal structure of gsk-3B in complex with the IMIDAZO[1,5- A]PYRIDINE-3-carboxamide inhibitor 16
6Y9S · Glycogen synthase kinase-3 beta: “Crystal structure of gsk-3B in complex with the IMIDAZO[1,5- A]PYRIDINE-3-carboxamide inhibitor 16”. X-ray diffraction, 1 ligand (OHK), 7 pockets (best druggability 0.84). MolNFT v1 #170508 on…
- PDB
- 6Y9S
- Type
- protein
- Length
- 684 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycogen synthase kinase-3 beta
- EC
- 2.7.11.26, 2.7.11.1
- UniProt
- P49841
- Ligands
- OHK
- Pockets
- 7 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycogen synthase kinase-3 beta (EC 2.7.11.26, 2.7.11.1) | protein | 344 | 35% helix, 19% strand | P49841 |
| B | Glycogen synthase kinase-3 beta (EC 2.7.11.26, 2.7.11.1) | protein | 340 | 36% helix, 19% strand | P49841 |
Ligands and binding sites
- OHK · ~{N}-(oxan-4-ylmethyl)-6-(5-propan-2-yloxypyridin-3-yl)imidazo[1,5-a]pyridine-3-carboxamide · ligand · 2 copies · chains A, B
- ACT · Acetate ion · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 867 | 0.84 | 0.86 | 92 | OHK |
| 2 | 177 | 0.60 | 0.82 | 29 | empty |
| 3 | 190 | 0.56 | 0.80 | 32 | empty |
| 4 | 83 | 0.36 | 0.76 | 20 | empty |
| 5 | 84 | 0.34 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1015 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 6Y9S · Crystal structure of GSK-3b in complex with the imidazo[1,5-a]pyridine-3-carboxamide… · the same entry in another collection · chain A against A, TM-score 1.00
- P49841 · AlphaFold monomer V2.0 prediction for glycogen synthase kinase-3 beta (P49841) · a predicted model of the same protein · chain A against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P49841
- Elsewhere: RCSB PDB 6Y9S · PDBe 6Y9S · UniProt P49841
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