Research workbench
Pseudokinase domain of mlkl bound to compound 1.
Analyse Pseudokinase domain of mlkl bound to compound 1. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KNJ
- Type
- protein
- Length
- 511 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mixed lineage kinase domain-like protein
- UniProt
- Q8NB16
- Ligands
- 6UX
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mixed lineage kinase domain-like protein | protein | 252 | 43% helix, 18% strand | Q8NB16 |
| B | Mixed lineage kinase domain-like protein | protein | 259 | 42% helix, 18% strand | Q8NB16 |
Ligands and binding sites
- 6UX · 1-[4-[methyl-[2-[(3-sulfamoylphenyl)amino]pyrimidin-4-yl]amino]phenyl]-3-[4-(trifluoromethyloxy)phenyl]urea · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 354 | 0.71 | 0.83 | 57 | empty |
| 2 | 439 | 0.67 | 0.79 | 37 | 6UX |
| 3 | 367 | 0.66 | 0.80 | 34 | 6UX |
| 4 | 75 | 0.41 | 0.79 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1297 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 5KNJ · Pseudokinase Domain of MLKL bound to Compound 1. · the same entry in another collection · chain A against A, TM-score 1.00
- Q8NB16 · AlphaFold monomer V2.0 prediction for mixed lineage kinase domain- like protein (Q8NB16) · a predicted model of the same protein · chain A against A, TM-score 0.89
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 Q8NB16
- Elsewhere: RCSB PDB 5KNJ · PDBe 5KNJ · UniProt Q8NB16
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