MolNFT v1 · #161327 · protein
Crystal structure of ULK2 in complexed with MRT68921
6QAV · SERINE/THREONINE-protein kinase ULK2: “Crystal structure of ULK2 in complexed with MRT68921”. X-ray diffraction, 2 ligands (HVH, NA), 5 pockets (best druggability 0.89). MolNFT v1 #161327 on GenesisL1: 3D structure, binding sites…
- PDB
- 6QAV
- Type
- protein
- Length
- 1,071 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
- HVH, NA
- Pockets
- 5 · best druggability 0.89
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase ULK2 (EC 2.7.11.1) | protein | 273 | 38% helix, 22% strand | Q8IYT8 |
| B | SERINE/THREONINE-protein kinase ULK2 (EC 2.7.11.1) | protein | 269 | 41% helix, 22% strand | Q8IYT8 |
| C | SERINE/THREONINE-protein kinase ULK2 (EC 2.7.11.1) | protein | 275 | 40% helix, 22% strand | Q8IYT8 |
| D | SERINE/THREONINE-protein kinase ULK2 (EC 2.7.11.1) | protein | 254 | 37% helix, 24% strand | Q8IYT8 |
Ligands and binding sites
- HVH · ~{N}-[3-[[5-cyclopropyl-2-[(2-methyl-3,4-dihydro-1~{H}-isoquinolin-6-yl)amino]pyrimidin-4-yl]amino]propyl]cyclobutanecarboxamide · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · chains B
- EDO · 1,2-ethanediol · additive · 15 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1180 | 0.89 | 0.91 | 130 | HVH, EDO, GOL |
| 2 | 1173 | 0.89 | 0.90 | 127 | HVH, EDO |
| 3 | 609 | 0.74 | 0.81 | 68 | empty |
| 4 | 337 | 0.67 | 0.81 | 41 | empty |
| 5 | 158 | 0.55 | 0.81 | 19 | empty |
Interfaces
4 interfaces between chains.
- A–B · 3083 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 2833 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 635 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 425 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6QAV · Crystal structure of ULK2 in complexed with MRT68921 · 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 C against A, TM-score 0.88
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 6QAV · PDBe 6QAV · UniProt Q8IYT8
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