Research workbench
Crystal structure of bruton's tyrosine kinase in complex with inhibitor 2e
Analyse Crystal structure of bruton's tyrosine kinase in complex with inhibitor 2e in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZZ4
- Type
- protein
- Length
- 1,574 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.9
- Source
- Homo sapiens
- Molecule
- Tyrosine-protein kinase BTK
- EC
- 2.7.10.2
- UniProt
- Q06187
- Ligands
- 9M3
- Pockets
- 20 · best druggability 0.70
Structure
x-ray diffraction · resolution 2.9 · 3 distinct chains · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine-protein kinase BTK (EC 2.7.10.2) | protein | 261 | 40% helix, 18% strand | Q06187 |
| B, D, F | Tyrosine-protein kinase BTK (EC 2.7.10.2) | protein | 263 | 39% helix, 18% strand | Q06187 |
| C, E | Tyrosine-protein kinase BTK (EC 2.7.10.2) | protein | 262 | 40% helix, 18% strand | Q06187 |
Ligands and binding sites
- 9M3 · N-[3-(4-amino-6-{[4-(morpholine-4-carbonyl) phenyl]amino}-1,3,5-triazin-2-yl)-2-methylphenyl]-4-tert-butylbenzamide · ligand · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 348 | 0.70 | 0.83 | 36 | 9M3 |
| 2 | 389 | 0.70 | 0.82 | 45 | 9M3 |
| 3 | 398 | 0.69 | 0.81 | 56 | 9M3 |
| 4 | 362 | 0.68 | 0.81 | 51 | 9M3 |
| 5 | 354 | 0.68 | 0.81 | 37 | 9M3 |
Interfaces
5 interfaces between chains.
- C–D · 686 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 670 Ų buried · 9 hydrogen bonds · protein-protein
- E–F · 632 Ų buried · 10 hydrogen bonds · protein-protein
- D–E · 240 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 232 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5ZZ4 · Crystal structure of BRUTON'S tyrosine kinase in complex with inhibitor 2E · the same entry in another collection · chain F against F, TM-score 1.00
- Q06187 · AlphaFold monomer V2.0 prediction for tyrosine-protein kinase btk (Q06187) · 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 Q06187
- Elsewhere: RCSB PDB 5ZZ4 · PDBe 5ZZ4 · UniProt Q06187
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