Research workbench
Crystal structure of murine IRE1 in complex with OICR464 inhibitor
Analyse Crystal structure of murine IRE1 in complex with OICR464 inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PL4
- Type
- protein
- Length
- 1,530 residues
- Chains
- 4
- 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
- Q9EQY0
- Ligands
- ADP, 31K, PEU, MG
- Pockets
- 16 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 12% 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 | 385 | 43% helix, 11% strand | Q9EQY0 |
| B, C | SERINE/THREONINE-protein KINASE/ENDORIBONUCLEASE IRE1 (EC 2.7.11.1, 3.1.26.-) | protein | 384 | 42% helix, 13% strand | Q9EQY0 |
| D | SERINE/THREONINE-protein KINASE/ENDORIBONUCLEASE IRE1 (EC 2.7.11.1, 3.1.26.-) | protein | 377 | 42% helix, 12% strand | Q9EQY0 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- 31K · 2-methoxy-6-methyl-4-(4-methyl-3,4-dihydro-2H-1,4-benzoxazin-7-yl)phenol · ligand · chains A
- PEU · 2,5,8,11,14,17,20,23,26,29,32,35,38,41,44,47,50,53,56, 59,62,65,68,71,74,77,80-heptacosaoxadooctacontan-82-ol · ligand
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 973 | 0.77 | 0.79 | 92 | empty |
| 2 | 72 | 0.74 | 0.97 | 22 | empty |
| 3 | 327 | 0.66 | 0.81 | 37 | ADP, MG |
| 4 | 320 | 0.66 | 0.81 | 37 | ADP, MG |
| 5 | 319 | 0.66 | 0.81 | 37 | ADP, MG |
Interfaces
3 interfaces between chains.
- C–D · 885 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 475 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 82 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 4PL4 · Crystal structure of murine IRE1 in complex with OICR464 inhibitor · the same entry in another collection · chain D against D, TM-score 1.00
- Q9EQY0 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein KINASE/ENDORIBONUCLEASE… · a predicted model of the same protein · chain B against A, TM-score 0.96
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 Q9EQY0
- Elsewhere: RCSB PDB 4PL4 · PDBe 4PL4 · UniProt Q9EQY0
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