Research workbench
Optimization of microtubule affinity regulating kinase (mark) inhibitors with improved physical properties
Analyse Optimization of microtubule affinity regulating kinase (mark) inhibitors with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EAK
- Type
- protein
- Length
- 605 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein kinase MARK2
- EC
- 2.7.11.1, 2.7.11.26
- UniProt
- Q7KZI7
- Ligands
- 24R
- Pockets
- 7 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase MARK2 (EC 2.7.11.1, 2.7.11.26) | protein | 305 | 43% helix, 16% strand | Q7KZI7 |
| B | SERINE/THREONINE-protein kinase MARK2 (EC 2.7.11.1, 2.7.11.26) | protein | 300 | 44% helix, 15% strand | Q7KZI7 |
Ligands and binding sites
- 24R · N-[(1S,2R)-2-aminocyclohexyl]-4-[6-(1-methyl-1H-pyrazol-4-yl)pyrazolo[1,5-a]pyrimidin-3-yl]thiophene-2-carboxamide · ligand · 2 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 711 | 0.71 | 0.78 | 70 | 24R |
| 2 | 257 | 0.66 | 0.83 | 26 | 24R |
| 3 | 383 | 0.57 | 0.75 | 44 | empty |
| 4 | 209 | 0.50 | 0.76 | 27 | empty |
| 5 | 58 | 0.45 | 0.83 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 332 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5EAK · Optimization of Microtubule Affinity Regulating Kinase (MARK) Inhibitors with Improved… · the same entry in another collection · chain A against A, TM-score 1.00
- Q7KZI7 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase MARK2 (Q7KZI7) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q7KZI7
- Elsewhere: RCSB PDB 5EAK · PDBe 5EAK · UniProt Q7KZI7
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