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Crystal structure of S6K1 kinase domain in complex with a pyrazolopyrimidine derivative 4-[4-(1H-benzimidazol-2-YL)PIPERIDIN-1- yl]-1H-PYRAZOLO[3,4-D]PYRIMIDINE
Analyse Crystal structure of S6K1 kinase domain in complex with a pyrazolopyrimidine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WF5
- Type
- protein
- Length
- 278 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribosomal protein S6 kinase beta-1
- EC
- 2.7.11.1
- UniProt
- P23443
- Ligands
- FZ8, ZN
- Pockets
- 3 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribosomal protein S6 kinase beta-1 (EC 2.7.11.1) | protein | 278 | 37% helix, 17% strand | P23443 |
Ligands and binding sites
- FZ8 · 4-[4-(1H-benzimidazol-2-yl)piperidin-1-yl]-1H-pyrazolo[3,4-d]pyrimidine · ligand · chains A
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 286 | 0.74 | 0.87 | 36 | FZ8 |
| 2 | 152 | 0.55 | 0.81 | 25 | empty |
| 3 | 57 | 0.28 | 0.74 | 14 | empty |
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 3WF5 · Crystal structure of S6K1 kinase domain in complex with a pyrazolopyrimidine derivative… · the same entry in another collection · chain A against A, TM-score 1.00
- P23443 · AlphaFold monomer V2.0 prediction for ribosomal protein S6 kinase beta-1 (P23443) · a predicted model of the same protein · chain A against A, TM-score 0.93
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 P23443
- Elsewhere: RCSB PDB 3WF5 · PDBe 3WF5 · UniProt P23443
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