Research workbench
Crystal structure of RIP1 kinase with a BENZO[B][1,4]OXAZEPIN-4-one
Analyse Crystal structure of RIP1 kinase with a BENZO[B][1,4]OXAZEPIN-4-one in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HX6
- Type
- protein
- Length
- 523 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Receptor-interacting SERINE/THREONINE-protein kinase 1
- EC
- 2.7.11.1
- UniProt
- Q13546
- Ligands
- 65U
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Receptor-interacting SERINE/THREONINE-protein kinase 1 (EC 2.7.11.1) | protein | 259 | 42% helix, 17% strand | Q13546 |
| B | Receptor-interacting SERINE/THREONINE-protein kinase 1 (EC 2.7.11.1) | protein | 264 | 43% helix, 14% strand | Q13546 |
Ligands and binding sites
- 65U · 5-benzyl-N-[(3S)-5-methyl-4-oxo-2,3,4,5-tetrahydro-1,5-benzoxazepin-3-yl]-1,2-oxazole-3-carboxamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 932 | 0.75 | 0.78 | 77 | empty |
| 2 | 361 | 0.73 | 0.84 | 46 | 65U |
| 3 | 207 | 0.71 | 0.87 | 31 | 65U |
| 4 | 171 | 0.64 | 0.85 | 24 | empty |
| 5 | 70 | 0.37 | 0.78 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 487 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5HX6 · Crystal structure of RIP1 kinase with a benzo[b][1,4]oxazepin-4-one · the same entry in another collection · chain A against A, TM-score 1.00
- Q13546 · AlphaFold monomer V2.0 prediction for receptor-interacting SERINE/THREONINE-protein… · a predicted model of the same protein · chain A against A, TM-score 0.95
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 Q13546
- Elsewhere: RCSB PDB 5HX6 · PDBe 5HX6 · UniProt Q13546
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