Research workbench
EGFR kinase (T790M/V948R) in complex with osimertinib and jbj-09-063
Analyse EGFR kinase (T790M/V948R) in complex with osimertinib and 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
- 7JXW
- Type
- protein
- Length
- 1,159 residues
- Chains
- 4
- 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
- YY3, VNS
- Pockets
- 18 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 287 | 43% helix, 16% strand | P00533 |
| A | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 288 | 43% helix, 17% strand | P00533 |
| C | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 293 | 43% helix, 17% strand | P00533 |
| B | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 291 | 43% helix, 16% strand | P00533 |
Ligands and binding sites
- 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 · 4 copies · chains D, A, C, B
- 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 · 4 copies · chains D, A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1071 | 0.85 | 0.86 | 79 | empty |
| 2 | 412 | 0.78 | 0.87 | 55 | YY3, VNS |
| 3 | 383 | 0.78 | 0.87 | 44 | YY3, VNS |
| 4 | 598 | 0.78 | 0.84 | 52 | empty |
| 5 | 409 | 0.75 | 0.84 | 45 | YY3, VNS |
Interfaces
5 interfaces between chains.
- D–B · 622 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 575 Ų buried · 2 hydrogen bonds · protein-protein
- D–C · 445 Ų buried · 3 hydrogen bonds · protein-protein
- D–A · 419 Ų buried · 2 hydrogen bonds · protein-protein
- C–B · 398 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 7JXW · EGFR kinase (T790M/V948R) in complex with osimertinib and JBJ-09-063 · the same entry in another collection · chain B against B, TM-score 1.00
- P00533 · AlphaFold monomer V2.0 prediction for epidermal growth factor receptor (P00533) · a predicted model of the same protein · chain D 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 7JXW · PDBe 7JXW · UniProt P00533
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.