MolNFT v1 · #108967 · protein
Structure of ULK1 bound to a potent inhibitor
4WNP · SERINE/THREONINE-protein kinase ULK1: “Structure of ULK1 bound to a potent inhibitor”. X-ray diffraction, 1 ligand (3RJ), 10 pockets (best druggability 0.74). MolNFT v1 #108967 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 4WNP
- Type
- protein
- Length
- 1,092 residues
- Chains
- 4
- 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
- 3RJ
- Pockets
- 10 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 38% 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, 20% strand | O75385 |
| B, D | SERINE/THREONINE-protein kinase ULK1 (EC 2.7.11.1) | protein | 273 | 36% helix, 21% strand | O75385 |
| C | SERINE/THREONINE-protein kinase ULK1 (EC 2.7.11.1) | protein | 272 | 38% helix, 21% strand | O75385 |
Ligands and binding sites
- 3RJ · N~2~-(1H-benzimidazol-6-yl)-N~4~-(5-cyclobutyl-1H-pyrazol-3-yl)quinazoline-2,4-diamine · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 806 | 0.74 | 0.79 | 76 | empty |
| 2 | 488 | 0.70 | 0.80 | 58 | empty |
| 3 | 671 | 0.70 | 0.78 | 56 | GOL |
| 4 | 320 | 0.68 | 0.82 | 31 | 3RJ |
| 5 | 324 | 0.68 | 0.82 | 31 | 3RJ |
Interfaces
3 interfaces between chains.
- B–D · 825 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 583 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 361 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (phosphorylation).
Compared structures
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 4WNP · PDBe 4WNP · UniProt O75385
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