Research workbench
Crystal structure of bruton agammaglobulinemia tyrosine kinase complexed with bms-809959 aka 4-tert-butyl-N-[2-me thyl-3-(6-{[4- (morpholine-4-CARBONYL)PHENYL]AMINO}-9H- purin-2-YL)PHENYL]BENZAMIDE
Analyse Crystal structure of bruton agammaglobulinemia tyrosine kinase complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NWM
- Type
- protein
- Length
- 524 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosine-protein kinase btk
- EC
- 2.7.10.2
- UniProt
- Q06187
- Ligands
- 2P5
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Tyrosine-protein kinase btk (EC 2.7.10.2) | protein | 262 | 42% helix, 18% strand | Q06187 |
Ligands and binding sites
- 2P5 · 4-tert-butyl-N-[2-methyl-3-(6-{[4-(morpholin-4-ylcarbonyl)phenyl]amino}-7H-purin-2-yl)phenyl]benzamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1118 | 0.78 | 0.80 | 82 | 2P5 |
| 2 | 897 | 0.75 | 0.78 | 81 | 2P5 |
| 3 | 54 | 0.55 | 0.89 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 346 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 4NWM · Crystal structure of Bruton agammaglobulinemia tyrosine kinase complexed with BMS-809959… · the same entry in another collection · chain A against A, TM-score 1.00
- Q06187 · AlphaFold monomer V2.0 prediction for tyrosine-protein kinase btk (Q06187) · a predicted model of the same protein · chain B 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 4NWM · PDBe 4NWM · UniProt Q06187
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