Research workbench
Crystal structure of mouse btk kinase domain in complex with compound 9A
Analyse Crystal structure of mouse btk kinase domain in complex with compound 9A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MNY
- Type
- protein
- Length
- 505 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosine-protein kinase
- EC
- 2.7.10.2
- UniProt
- Q7TMU1
- Ligands
- JVP
- Pockets
- 4 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine-protein kinase (EC 2.7.10.2) | protein | 252 | 43% helix, 19% strand | Q7TMU1 |
| B | Tyrosine-protein kinase (EC 2.7.10.2) | protein | 253 | 43% helix, 18% strand | Q7TMU1 |
Ligands and binding sites
- JVP · 5-amino-1-[(3R)-1-cyanopiperidin-3-yl]-3-[4-(2,4-difluorophenoxy)phenyl]-1H-pyrazole-4-carboxamide · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1083 | 0.82 | 0.83 | 88 | empty |
| 2 | 279 | 0.70 | 0.85 | 41 | JVP |
| 3 | 54 | 0.43 | 0.83 | 16 | empty |
| 4 | 78 | 0.34 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 681 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6MNY · Crystal structure of mouse BTK kinase domain in complex with compound 9a · 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 Q7TMU1
- Elsewhere: RCSB PDB 6MNY · PDBe 6MNY · UniProt Q7TMU1
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