Research workbench
Crystal structure of S6K1 kinase domain in complex with a pyrimidine derivative pf-4708671 2-{[4-(5-ethylpyrimidin-4-YL)PIPERAZIN-1- YL]METHYL}-5-(trifluoromethyl)-1H-benzimidazole
Analyse Crystal structure of S6K1 kinase domain in complex with a pyrimidine derivative… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WE4
- Type
- protein
- Length
- 287 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
- 5FI, ZN
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribosomal protein S6 kinase beta-1 (EC 2.7.11.1) | protein | 287 | 40% helix, 16% strand | P23443 |
Ligands and binding sites
- 5FI · 2-{[4-(5-ethylpyrimidin-4-yl)piperazin-1-yl]methyl}-5-(trifluoromethyl)-1H-benzimidazole · 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
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 326 | 0.73 | 0.85 | 35 | 5FI |
| 2 | 221 | 0.63 | 0.83 | 26 | empty |
| 3 | 50 | 0.37 | 0.80 | 15 | empty |
| 4 | 81 | 0.33 | 0.74 | 17 | empty |
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 3WE4 · Crystal structure of S6K1 kinase domain in complex with a pyrimidine 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 0.94
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 3WE4 · PDBe 3WE4 · UniProt P23443
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