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Crystal structure of RIP1 kinase bound to inhibitor
Analyse Crystal structure of RIP1 kinase bound to inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6C3E
- Type
- protein
- Length
- 517 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
- EJY
- Pockets
- 7 · best druggability 0.80
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 | 258 | 43% helix, 17% strand | Q13546 |
| B | Receptor-interacting SERINE/THREONINE-protein kinase 1 (EC 2.7.11.1) | protein | 259 | 41% helix, 15% strand | Q13546 |
Ligands and binding sites
- EJY · 2-benzyl-5-nitro-1H-benzimidazole · 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 | 126 | 0.80 | 0.97 | 22 | EJY |
| 2 | 185 | 0.76 | 0.92 | 29 | EJY |
| 3 | 641 | 0.68 | 0.77 | 52 | empty |
| 4 | 212 | 0.52 | 0.77 | 36 | empty |
| 5 | 56 | 0.39 | 0.80 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 440 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6C3E · Crystal structure of RIP1 kinase bound to inhibitor · 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 B 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 6C3E · PDBe 6C3E · UniProt Q13546
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