Research workbench
Crystal structure of RIP1 kinase in complex with necrostatin-4
Analyse Crystal structure of RIP1 kinase in complex with necrostatin-4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ITJ
- Type
- protein
- Length
- 537 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
- 1HX, IOD
- Pockets
- 8 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 43% 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 | 261 | 43% helix, 16% strand | Q13546 |
| B | Receptor-interacting SERINE/THREONINE-protein kinase 1 (EC 2.7.11.1) | protein | 276 | 43% helix, 17% strand | Q13546 |
Ligands and binding sites
- 1HX · N-[(1S)-1-(2-chloro-6-fluorophenyl)ethyl]-5-cyano-1-methyl-1H-pyrrole-2-carboxamide · ligand · 2 copies · chains A, B
- IOD · Iodide ion · ion · 9 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 164 | 0.81 | 0.96 | 28 | 1HX |
| 2 | 849 | 0.75 | 0.79 | 85 | IOD |
| 3 | 243 | 0.73 | 0.87 | 40 | 1HX, IOD |
| 4 | 105 | 0.47 | 0.80 | 24 | IOD |
| 5 | 52 | 0.34 | 0.78 | 11 | IOD |
Interfaces
1 interface between chains.
- A–B · 556 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4ITJ · Crystal structure of RIP1 kinase in complex with necrostatin-4 · 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 4ITJ · PDBe 4ITJ · UniProt Q13546
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