Research workbench
Crystal structure of RIP1 kinase in complex with a pyrrolidine
Analyse Crystal structure of RIP1 kinase in complex with a pyrrolidine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OCQ
- Type
- protein
- Length
- 536 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
- M5J, SO4
- Pockets
- 11 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 41% 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 | 262 | 42% helix, 17% strand | Q13546 |
| B | Receptor-interacting SERINE/THREONINE-protein kinase 1 (EC 2.7.11.1) | protein | 274 | 40% helix, 16% strand | Q13546 |
Ligands and binding sites
- M5J · 1-[(2S)-2-(3-fluorophenyl)pyrrolidin-1-yl]-2,2-dimethylpropan-1-one · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 130 | 0.80 | 0.97 | 20 | M5J |
| 2 | 146 | 0.79 | 0.96 | 20 | M5J |
| 3 | 279 | 0.65 | 0.82 | 37 | empty |
| 4 | 329 | 0.65 | 0.80 | 40 | empty |
| 5 | 71 | 0.54 | 0.86 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 616 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6OCQ · Crystal structure of RIP1 kinase in complex with a pyrrolidine · 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 0.96
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 6OCQ · PDBe 6OCQ · UniProt Q13546
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