Research workbench
Crystal structure of ULK1 in complexed with pf-03814735
Analyse Crystal structure of ULK1 in complexed with pf-03814735 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QAS
- Type
- protein
- Length
- 547 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein kinase ULK1
- EC
- 2.7.11.1
- UniProt
- O75385
- Ligands
- 34W, SO4
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase ULK1 (EC 2.7.11.1) | protein | 274 | 39% helix, 21% strand | O75385 |
| B | SERINE/THREONINE-protein kinase ULK1 (EC 2.7.11.1) | protein | 273 | 39% helix, 21% strand | O75385 |
Ligands and binding sites
- 34W · N-{2-[(1S,4R)-6-{[4-(cyclobutylamino)-5-(trifluoromethyl)pyrimidin-2-yl]amino}-1,2,3,4-tetrahydro-1,4-epiminonaphthalen-9-yl]-2-oxoethyl}acetamide · ligand · 3 copies · chains A, B
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 12 copies · chains A, B
- GOL · Glycerol · additive · 11 copies · chains A, B
- CIT · Citric acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 726 | 0.79 | 0.83 | 84 | CIT, GOL, 34W, EDO |
| 2 | 276 | 0.69 | 0.84 | 32 | CIT, GOL, 34W |
| 3 | 67 | 0.33 | 0.76 | 14 | EDO |
| 4 | 52 | 0.32 | 0.77 | 14 | GOL |
| 5 | 53 | 0.31 | 0.77 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 496 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (phosphorylation).
Compared structures
- 6QAS · Crystal structure of ULK1 in complexed with PF-03814735 · the same entry in another collection · chain A against A, TM-score 1.00
- O75385 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase ULK1 (O75385) · a predicted model of the same protein · chain B 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 O75385
- Elsewhere: RCSB PDB 6QAS · PDBe 6QAS · UniProt O75385
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