Research workbench
Crystal structure of bruton agammaglobulinemia tyrosine kinase complexed with bms-824171 aka 6-[(3R)-3-(4-tert-bu tylbenzamido) piperidin-1-yl]-2-{[4-(morpholine-4-carbonyl) PHENYL]AMINO}PYRIDINE- 3-carboxamide
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
- 5BPY
- Type
- protein
- Length
- 510 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
- 4UQ
- Pockets
- 5 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine-protein kinase btk (EC 2.7.10.2) | protein | 263 | 42% helix, 18% strand | Q06187 |
| B | Tyrosine-protein kinase btk (EC 2.7.10.2) | protein | 247 | 44% helix, 17% strand | Q06187 |
Ligands and binding sites
- 4UQ · 6-{(3R)-3-[(4-tert-butylbenzoyl)amino]piperidin-1-yl}-2-{[4-(morpholin-4-ylcarbonyl)phenyl]amino}pyridine-3-carboxamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 446 | 0.63 | 0.77 | 51 | 4UQ |
| 2 | 288 | 0.61 | 0.79 | 35 | 4UQ |
| 3 | 154 | 0.44 | 0.75 | 26 | empty |
| 4 | 72 | 0.39 | 0.78 | 15 | empty |
| 5 | 60 | 0.38 | 0.79 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 516 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 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 5BPY · PDBe 5BPY · UniProt Q06187
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