Research workbench
Crystal structure of EGFR kinase domain T790M mutation in compex with hki-272
Analyse Crystal structure of EGFR kinase domain T790M mutation in compex with hki-272 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2JIV
- Type
- protein
- Length
- 542 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Epidermal growth factor receptor
- EC
- 2.7.1.112, 2.7.10.1
- UniProt
- P00533
- Ligands
- HKI, CL
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Epidermal growth factor receptor (EC 2.7.1.112, 2.7.10.1) | protein | 270 | 33% helix, 10% strand | P00533 |
| B | Epidermal growth factor receptor (EC 2.7.1.112, 2.7.10.1) | protein | 272 | 33% helix, 8% strand | P00533 |
Ligands and binding sites
- HKI · N-(4-{[3-chloro-4-(pyridin-2-ylmethoxy)phenyl]amino}-3-cyano-7-ethoxyquinolin-6-yl)-4-(dimethylamino)butanamide · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 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 | 289 | 0.83 | 0.94 | 38 | CL |
| 2 | 761 | 0.78 | 0.82 | 80 | HKI |
| 3 | 656 | 0.76 | 0.82 | 76 | HKI |
| 4 | 232 | 0.49 | 0.75 | 28 | empty |
| 5 | 88 | 0.46 | 0.80 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1280 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 2JIV · Crystal structure of EGFR kinase domain T790M mutation in compex with HKI-272 · the same entry in another collection · chain A against A, TM-score 1.00
- P00533 · AlphaFold monomer V2.0 prediction for epidermal growth factor receptor (P00533) · a predicted model of the same protein · chain A against A, TM-score 0.92
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 2JIV · PDBe 2JIV · UniProt P00533
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