Research workbench
Crystal structure of RIP1 kinase in complex with necrostatin-3 analog
Analyse Crystal structure of RIP1 kinase in complex with necrostatin-3 analog in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ITI
- Type
- protein
- Length
- 542 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
- 1HW
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Receptor-interacting SERINE/THREONINE-protein kinase 1 (EC 2.7.11.1) | protein | 272 | 37% helix, 15% strand | Q13546 |
| B | Receptor-interacting SERINE/THREONINE-protein kinase 1 (EC 2.7.11.1) | protein | 270 | 43% helix, 16% strand | Q13546 |
Ligands and binding sites
- 1HW · 1-{(3S,3aS)-3-[3-fluoro-4-(trifluoromethoxy)phenyl]-8-methoxy-3,3a,4,5-tetrahydro-2H-benzo[g]indazol-2-yl}-2-hydroxyethanone · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 213 | 0.81 | 0.94 | 30 | 1HW |
| 2 | 211 | 0.81 | 0.94 | 28 | 1HW |
| 3 | 861 | 0.72 | 0.77 | 78 | empty |
| 4 | 53 | 0.33 | 0.78 | 14 | empty |
| 5 | 76 | 0.31 | 0.73 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 769 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 4ITI · Crystal structure of RIP1 kinase in complex with necrostatin-3 analog · 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 0.94
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 4ITI · PDBe 4ITI · UniProt Q13546
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