MolNFT v1 · #111722 · protein
Crystal structure of human phosphorylated IRE1ALPHA in complex with a type III kinase inhibitor (GSK2850163A)
4YZ9 · SERINE/THREONINE-protein KINASE/ENDORIBONUCLEASE IRE1: “Crystal structure of human phosphorylated IRE1ALPHA in complex with a type III kinase inhibitor (GSK2850163A)”. X-ray diffraction, 1 ligand (4K7), 12 pockets (best druggability…
- PDB
- 4YZ9
- Type
- protein
- Length
- 1,134 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein KINASE/ENDORIBONUCLEASE IRE1
- EC
- 2.7.11.1, 3.1.26.-
- UniProt
- O75460
- Ligands
- 4K7
- Pockets
- 12 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein KINASE/ENDORIBONUCLEASE IRE1 (EC 2.7.11.1, 3.1.26.-) | protein | 381 | 48% helix, 14% strand | O75460 |
| B | SERINE/THREONINE-protein KINASE/ENDORIBONUCLEASE IRE1 (EC 2.7.11.1, 3.1.26.-) | protein | 375 | 45% helix, 15% strand | O75460 |
| C | SERINE/THREONINE-protein KINASE/ENDORIBONUCLEASE IRE1 (EC 2.7.11.1, 3.1.26.-) | protein | 378 | 48% helix, 14% strand | O75460 |
Ligands and binding sites
- 4K7 · (5R)-2-(3,4-dichlorobenzyl)-N-(4-methylbenzyl)-2,7-diazaspiro[4.5]decane-7-carboxamide · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1092 | 0.80 | 0.81 | 108 | empty |
| 2 | 329 | 0.79 | 0.90 | 35 | 4K7 |
| 3 | 264 | 0.77 | 0.89 | 28 | 4K7 |
| 4 | 351 | 0.74 | 0.85 | 42 | 4K7 |
| 5 | 460 | 0.68 | 0.80 | 56 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1050 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 871 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 12 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4YZ9 · Crystal Structure of human phosphorylated IRE1alpha in complex with a type III kinase… · the same entry in another collection · chain A against A, TM-score 1.00
- O75460 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein KINASE/ENDORIBONUCLEASE… · a predicted model of the same protein · chain B 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 O75460
- Elsewhere: RCSB PDB 4YZ9 · PDBe 4YZ9 · UniProt O75460
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