MolNFT v1 · #140067 · protein
The structure of human btk kinase domain in complex with a covalent inhibitor
5XYZ · Tyrosine-protein kinase btk: “The structure of human btk kinase domain in complex with a covalent inhibitor”. X-ray diffraction, 1 ligand (GYL), 6 pockets (best druggability 0.77). MolNFT v1 #140067 on GenesisL1: 3D structure…
- PDB
- 5XYZ
- Type
- protein
- Length
- 464 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
- GYL
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine-protein kinase btk (EC 2.7.10.2) | protein | 230 | 40% helix, 17% strand | Q06187 |
| B | Tyrosine-protein kinase btk (EC 2.7.10.2) | protein | 234 | 41% helix, 15% strand | Q06187 |
Ligands and binding sites
- GYL · N-[3-(5-{[(2-chloro-6-fluorophenyl)methyl]amino}-1H-1, 2,4-triazol-3-yl)phenyl]propanamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1060 | 0.77 | 0.79 | 90 | empty |
| 2 | 248 | 0.59 | 0.79 | 26 | GYL |
| 3 | 223 | 0.58 | 0.79 | 26 | GYL |
| 4 | 102 | 0.55 | 0.84 | 18 | empty |
| 5 | 170 | 0.49 | 0.77 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 873 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5XYZ · The structure of human BTK kinase domain in complex with a covalent inhibitor · 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 A against A, TM-score 0.95
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 5XYZ · PDBe 5XYZ · UniProt Q06187
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