Research workbench
Crystal structure of the kinase domain of BRUTON'S tyrosine kinase with mutations in the activation loop
Analyse Crystal structure of the kinase domain of BRUTON'S tyrosine kinase with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Y95
- Type
- protein
- Length
- 1,063 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Non-specific protein-tyrosine kinase
- EC
- 2.7.10.2
- UniProt
- Q3ZC95
- Ligands
- 746
- Pockets
- 13 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Non-specific protein-tyrosine kinase (EC 2.7.10.2) | protein | 266 | 44% helix, 17% strand | Q3ZC95 |
| D | Non-specific protein-tyrosine kinase (EC 2.7.10.2) | protein | 265 | 42% helix, 17% strand | Q3ZC95 |
Ligands and binding sites
- 746 · 4-tert-butyl-N-[2-methyl-3-(4-methyl-6-{[4-(morpholin-4-ylcarbonyl)phenyl]amino}-5-oxo-4,5-dihydropyrazin-2-yl)phenyl]benzamide · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 8 copies · chains A, B, C, D
- BME · Beta-mercaptoethanol · additive · 3 copies · chains A, B, C
- PE4 · 2-{2-[2-(2-{2-[2-(2-ethoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethanol · additive · 2 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 408 | 0.71 | 0.82 | 45 | 746, BME |
| 2 | 375 | 0.71 | 0.83 | 40 | 746, BME |
| 3 | 466 | 0.71 | 0.81 | 54 | 746, GOL |
| 4 | 462 | 0.71 | 0.81 | 55 | 746, BME |
| 5 | 414 | 0.68 | 0.80 | 45 | GOL |
Interfaces
3 interfaces between chains.
- B–D · 613 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 609 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 584 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4Y95 · Crystal structure of the kinase domain of Bruton's tyrosine kinase with mutations in the… · 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 Q3ZC95
- Elsewhere: RCSB PDB 4Y95 · PDBe 4Y95 · UniProt Q3ZC95
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