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Btk kinase domain with inhibitor 1
Analyse Btk kinase domain with inhibitor 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FBN
- Type
- protein
- Length
- 511 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
- 5WE, 5WF, CL
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Tyrosine-protein kinase btk (EC 2.7.10.2) | protein | 256 | 43% helix, 18% strand | Q06187 |
| D | Tyrosine-protein kinase btk (EC 2.7.10.2) | protein | 255 | 43% helix, 18% strand | Q06187 |
Ligands and binding sites
- 5WE · 4-[8-azanyl-3-[(2~{S})-1-[4-(dimethylamino) butanoyl]pyrrolidin-2-yl]imidazo[1,5-a]pyrazin-1-yl]-~{N}-(1,3-thiazol-2-yl)benzamide · ligand · 4 copies · chains C, D
- 5WF · 4-[8-azanyl-3-[(3~{R})-1-(3-methyloxetan-3-yl)carbonylpiperidin-3-yl]imidazo[1,5-a]pyrazin-1-yl]-~{N}-[4-(trifluoromethyl)pyridin-2-yl]benzamide · ligand · 2 copies · chains C, D
- CL · Chloride ion · ion · 2 copies · chains C, D
- EDO · 1,2-ethanediol · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 250 | 0.71 | 0.86 | 35 | 5WF |
| 2 | 237 | 0.70 | 0.86 | 32 | 5WF |
| 3 | 333 | 0.50 | 0.72 | 33 | 5WE |
| 4 | 99 | 0.45 | 0.79 | 23 | empty |
| 5 | 98 | 0.37 | 0.75 | 19 | empty |
Interfaces
1 interface between chains.
- C–D · 91 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
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 5FBN · PDBe 5FBN · UniProt Q06187
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