Research workbench
Crystal structure of cot kinase domain in complex with 5-(2-amino-5- (quinolin-3-YL)PYRIDIN-3-yl)-1,3,4-oxadiazole-2(3H)-thione
Analyse Crystal structure of cot kinase domain in complex with 5-(2-amino-5… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Y83
- Type
- protein
- Length
- 894 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mitogen-activated protein kinase kinase kinase 8
- EC
- 2.7.11.25
- UniProt
- P41279
- Ligands
- 49B
- Pockets
- 13 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mitogen-activated protein kinase kinase kinase 8 (EC 2.7.11.25) | protein | 299 | 34% helix, 22% strand | P41279 |
| B | Mitogen-activated protein kinase kinase kinase 8 (EC 2.7.11.25) | protein | 302 | 34% helix, 22% strand | P41279 |
| C | Mitogen-activated protein kinase kinase kinase 8 (EC 2.7.11.25) | protein | 293 | 35% helix, 21% strand | P41279 |
Ligands and binding sites
- 49B · 5-[2-amino-5-(quinolin-3-yl)pyridin-3-yl]-1,3,4-oxadiazole-2(3H)-thione · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1171 | 0.74 | 0.77 | 112 | empty |
| 2 | 501 | 0.74 | 0.83 | 73 | 49B |
| 3 | 57 | 0.72 | 0.98 | 23 | empty |
| 4 | 166 | 0.67 | 0.87 | 37 | 49B |
| 5 | 238 | 0.66 | 0.83 | 45 | 49B |
Interfaces
3 interfaces between chains.
- A–B · 269 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 124 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 40 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4Y83 · Crystal structure of COT kinase domain in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- P41279 · AlphaFold monomer V2.0 prediction for mitogen-activated protein kinase kinase kinase 8… · a predicted model of the same protein · chain C against A, TM-score 0.97
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 P41279
- Elsewhere: RCSB PDB 4Y83 · PDBe 4Y83 · UniProt P41279
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