Research workbench
Bone marrow tyrosine kinase in chromosome X in complex with a newly designed covalent inhibitor JS24
Analyse Bone marrow tyrosine kinase in chromosome X in complex with a newly designed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6I99
- Type
- protein
- Length
- 527 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytoplasmic tyrosine-protein kinase bmx
- EC
- 2.7.10.2
- UniProt
- P51813
- Ligands
- H88
- Pockets
- 9 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytoplasmic tyrosine-protein kinase bmx (EC 2.7.10.2) | protein | 266 | 38% helix, 21% strand | P51813 |
| B | Cytoplasmic tyrosine-protein kinase bmx (EC 2.7.10.2) | protein | 261 | 39% helix, 21% strand | P51813 |
Ligands and binding sites
- H88 · ~{N}-[2-methyl-5-[8-[4-(methylsulfonylamino)phenyl]-2-oxidanylidene-benzo[h][1,6]naphthyridin-1-yl]phenyl]-3-oxidanyl-propanamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 277 | 0.66 | 0.82 | 29 | H88 |
| 2 | 298 | 0.65 | 0.81 | 35 | H88 |
| 3 | 258 | 0.57 | 0.78 | 36 | empty |
| 4 | 151 | 0.55 | 0.81 | 21 | empty |
| 5 | 142 | 0.50 | 0.79 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1049 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6I99 · Bone Marrow Tyrosine Kinase in Chromosome X in complex with a newly designed covalent… · the same entry in another collection · chain A against A, TM-score 1.00
- P51813 · AlphaFold monomer V2.0 prediction for cytoplasmic tyrosine-protein kinase bmx (P51813) · a predicted model of the same protein · chain A against A, TM-score 0.92
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 P51813
- Elsewhere: RCSB PDB 6I99 · PDBe 6I99 · UniProt P51813
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