MolNFT v1 · #124791 · protein
Glycogen synthase kinase 3 beta complexed with BRD3731
5KPM · Glycogen synthase kinase-3 beta: “Glycogen synthase kinase 3 beta complexed with BRD3731”. X-ray diffraction, 1 ligand (6VM), 9 pockets (best druggability 0.76). MolNFT v1 #124791 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5KPM
- Type
- protein
- Length
- 691 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
- 6VM
- Pockets
- 9 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 34% 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 | 345 | 34% helix, 20% strand | P49841 |
| B | Glycogen synthase kinase-3 beta (EC 2.7.11.26, 2.7.11.1) | protein | 346 | 34% helix, 19% strand | P49841 |
Ligands and binding sites
- 6VM · (4~{S})-3-(2,2-dimethylpropyl)-4,7,7-trimethyl-4-phenyl-2,6,8,9-tetrahydropyrazolo[3,4-b]quinolin-5-one · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 496 | 0.76 | 0.83 | 46 | 6VM |
| 2 | 472 | 0.74 | 0.83 | 38 | 6VM |
| 3 | 368 | 0.62 | 0.78 | 40 | empty |
| 4 | 133 | 0.52 | 0.81 | 24 | empty |
| 5 | 99 | 0.48 | 0.81 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 1002 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 5KPM · Glycogen Synthase Kinase 3 beta Complexed with BRD3731 · the same entry in another collection · chain A against A, TM-score 1.00
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 5KPM · PDBe 5KPM · UniProt P49841
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