Research workbench
Crystal structure of ULK2 in complex with sbi-0206965
Analyse Crystal structure of ULK2 in complex with sbi-0206965 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YID
- Type
- protein
- Length
- 1,039 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein kinase ULK2
- EC
- 2.7.11.1
- UniProt
- Q8IYT8
- Ligands
- EDJ
- Pockets
- 11 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase ULK2 (EC 2.7.11.1) | protein | 259 | 37% helix, 23% strand | Q8IYT8 |
| B | SERINE/THREONINE-protein kinase ULK2 (EC 2.7.11.1) | protein | 264 | 36% helix, 23% strand | Q8IYT8 |
| C | SERINE/THREONINE-protein kinase ULK2 (EC 2.7.11.1) | protein | 259 | 37% helix, 23% strand | Q8IYT8 |
| D | SERINE/THREONINE-protein kinase ULK2 (EC 2.7.11.1) | protein | 257 | 37% helix, 22% strand | Q8IYT8 |
Ligands and binding sites
- EDJ · 2-({5-bromo-2-[(3,4,5-trimethoxyphenyl)amino]pyrimidin-4-yl}oxy)-N-methylbenzene-1-carboximidic acid · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1160 | 0.81 | 0.82 | 97 | EDJ |
| 2 | 514 | 0.70 | 0.79 | 43 | EDJ |
| 3 | 338 | 0.69 | 0.82 | 34 | EDJ |
| 4 | 341 | 0.67 | 0.81 | 34 | EDJ |
| 5 | 524 | 0.67 | 0.77 | 32 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2239 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 371 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 259 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 105 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 38 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6YID · Crystal structure of ULK2 in complex with SBI-0206965 · the same entry in another collection · chain D against D, TM-score 1.00
- Q8IYT8 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase ULK2 (Q8IYT8) · a predicted model of the same protein · chain D against A, TM-score 0.92
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 Q8IYT8
- Elsewhere: RCSB PDB 6YID · PDBe 6YID · UniProt Q8IYT8
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