MolNFT v1 · #103584 · protein
Crystal structure of murine IRE1 in complex with MKC9989 inhibitor
4PL3 · SERINE/THREONINE-protein KINASE/ENDORIBONUCLEASE IRE1: “Crystal structure of murine IRE1 in complex with MKC9989 inhibitor”. X-ray diffraction, 3 ligands (31J, ADP, MG), 9 pockets (best druggability 0.68). MolNFT v1 #103584 on…
- PDB
- 4PL3
- Type
- protein
- Length
- 771 residues
- Chains
- 2
- 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
- 31J, ADP, MG
- Pockets
- 9 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 13% 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 | 388 | 43% helix, 13% strand | Q9EQY0 |
| B | SERINE/THREONINE-protein KINASE/ENDORIBONUCLEASE IRE1 (EC 2.7.11.1, 3.1.26.-) | protein | 383 | 42% helix, 12% strand | Q9EQY0 |
Ligands and binding sites
- 31J · 7-hydroxy-6-methoxy-3-[2-(2-methoxyethoxy)ethyl]-4,8-dimethyl-2H-chromen-2-one · ligand · 2 copies · chains A, B
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 338 | 0.68 | 0.82 | 42 | ADP, MG |
| 2 | 333 | 0.68 | 0.82 | 40 | ADP, MG |
| 3 | 97 | 0.54 | 0.84 | 18 | empty |
| 4 | 195 | 0.46 | 0.74 | 32 | empty |
| 5 | 107 | 0.46 | 0.79 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 249 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 4PL3 · Crystal structure of murine IRE1 in complex with MKC9989 inhibitor · the same entry in another collection · chain A against A, 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 4PL3 · PDBe 4PL3 · UniProt Q9EQY0
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