MolNFT v1 · #158831 · protein
Crystal structure of the human mlkl pseudokinase domain bound to compound 2
6O5Z · Mixed lineage kinase domain-like protein: “Crystal structure of the human mlkl pseudokinase domain bound to compound 2”. X-ray diffraction, 1 ligand (LN4), 7 pockets (best druggability 0.72). MolNFT v1 #158831 on GenesisL1: 3D…
- PDB
- 6O5Z
- Type
- protein
- Length
- 531 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
- LN4
- Pockets
- 7 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mixed lineage kinase domain-like protein | protein | 271 | 40% helix, 18% strand | Q8NB16 |
| B | Mixed lineage kinase domain-like protein | protein | 260 | 41% helix, 17% strand | Q8NB16 |
Ligands and binding sites
- LN4 · 1-[2-fluoranyl-5-(trifluoromethyl)phenyl]-3-[4-[methyl-[2-[(3-sulfamoylphenyl)amino]pyrimidin-4-yl]amino]phenyl]urea · ligand · chains B
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 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 | 0.72 | 0.84 | 56 | EDO |
| 2 | 403 | 0.70 | 0.82 | 47 | LN4 |
| 3 | 331 | 0.69 | 0.82 | 40 | EDO |
| 4 | 138 | 0.45 | 0.77 | 29 | empty |
| 5 | 129 | 0.42 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1395 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6O5Z · Crystal Structure of the human MLKL pseudokinase domain bound to compound 2 · 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 0.87
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 6O5Z · PDBe 6O5Z · UniProt Q8NB16
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