Research workbench
EGFR L858R/V948R in complex with osimertinib and allosteric inhibitor jbj-09-063
Analyse EGFR L858R/V948R in complex with osimertinib and allosteric inhibitor jbj-09-063 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7K1H
- Type
- protein
- Length
- 1,743 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Epidermal growth factor receptor
- EC
- 2.7.10.1
- UniProt
- P00533
- Ligands
- VNS, YY3
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 5 distinct chains · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 291 | 41% helix, 17% strand | P00533 |
| A | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 291 | 41% helix, 17% strand | P00533 |
| C, F | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 290 | 41% helix, 19% strand | P00533 |
| D | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 292 | 40% helix, 17% strand | P00533 |
| E | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 289 | 41% helix, 17% strand | P00533 |
Ligands and binding sites
- VNS · (2R)-2-(5-fluoro-2-hydroxyphenyl)-2-{6-[4-(1-methylpiperidin-4-yl)phenyl]-1-oxo-1,3-dihydro-2H-isoindol-2-yl}-N-(1,3-thiazol-2-yl)acetamide · ligand · 6 copies · chains B, A, C, D, E, F
- YY3 · N-(2-{[2-(dimethylamino)ethyl](methyl)amino}-4-methoxy-5-{[4-(1-methyl-1H-indol-3-yl)pyrimidin-2-yl]amino}phenyl)prop-2-enamide · ligand · 6 copies · chains B, A, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1190 | 0.82 | 0.83 | 116 | VNS, YY3 |
| 2 | 636 | 0.78 | 0.83 | 63 | VNS, YY3 |
| 3 | 1153 | 0.77 | 0.79 | 99 | VNS, YY3 |
| 4 | 327 | 0.75 | 0.86 | 28 | empty |
| 5 | 548 | 0.75 | 0.82 | 52 | VNS, YY3 |
Interfaces
7 interfaces between chains.
- B–A · 1631 Ų buried · 16 hydrogen bonds · protein-protein
- C–F · 1629 Ų buried · 16 hydrogen bonds · protein-protein
- D–E · 1555 Ų buried · 16 hydrogen bonds · protein-protein
- B–E · 709 Ų buried · 6 hydrogen bonds · protein-protein
- B–F · 391 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent (covalent ligand).
Compared structures
- 7K1H · EGFR L858R/V948R in complex with osimertinib and allosteric inhibitor JBJ-09-063 · the same entry in another collection · chain C against C, TM-score 1.00
- P00533 · AlphaFold monomer V2.0 prediction for epidermal growth factor receptor (P00533) · a predicted model of the same protein · chain F against A, TM-score 0.90
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 P00533
- Elsewhere: RCSB PDB 7K1H · PDBe 7K1H · UniProt P00533
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