Research workbench
Structure of Mnk1 in complex with DS12881479
Analyse Structure of Mnk1 in complex with DS12881479 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WVD
- Type
- protein
- Length
- 453 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3
- Source
- Homo sapiens
- Molecule
- MAP kinase interacting serine/threonine kinase 1
- UniProt
- B5BUJ6
- Ligands
- 7UX, SO4
- Pockets
- 2 · best druggability 0.64
Structure
x-ray diffraction · resolution 3 · 2 distinct chains · 33% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MAP kinase interacting serine/threonine kinase 1 | protein | 241 | 35% helix, 21% strand | B5BUJ6 |
| B | MAP kinase interacting serine/threonine kinase 1 | protein | 212 | 30% helix, 24% strand | B5BUJ6 |
Ligands and binding sites
- 7UX · 1-methyl-N-(5-phenyl-1,3-thiazol-2-yl)piperidine-4-carboxamide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 96 | 0.64 | 0.89 | 24 | 7UX |
| 2 | 174 | 0.58 | 0.81 | 27 | 7UX |
Interfaces
1 interface between chains.
- A–B · 1451 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 5WVD · Structure of MNK1 in complex with DS12881479 · 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 B5BUJ6
- Elsewhere: RCSB PDB 5WVD · PDBe 5WVD · UniProt B5BUJ6
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