Research workbench
EGFR kinase (T790M/V948R) in complex with AZ5104
Analyse EGFR kinase (T790M/V948R) in complex with AZ5104 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7JXL
- Type
- protein
- Length
- 1,163 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.4
- Source
- Homo sapiens
- Molecule
- Epidermal growth factor receptor
- EC
- 2.7.10.1
- UniProt
- P00533
- Ligands
- VO7
- Pockets
- 16 · best druggability 0.81
Structure
x-ray diffraction · resolution 2.4 · 4 distinct chains · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 292 | 45% helix, 17% strand | P00533 |
| A | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 294 | 41% helix, 17% strand | P00533 |
| C | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 292 | 43% helix, 18% strand | P00533 |
| B | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 285 | 44% helix, 18% strand | P00533 |
Ligands and binding sites
- VO7 · N-(2-{[2-(dimethylamino)ethyl](methyl)amino}-5-{[4-(1H-indol-3-yl)pyrimidin-2-yl]amino}-4-methoxyphenyl) propanamide · ligand · 4 copies · chains D, C, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1156 | 0.81 | 0.82 | 87 | empty |
| 2 | 1175 | 0.80 | 0.81 | 100 | VO7 |
| 3 | 820 | 0.70 | 0.76 | 61 | empty |
| 4 | 287 | 0.68 | 0.83 | 44 | VO7 |
| 5 | 381 | 0.65 | 0.79 | 41 | VO7 |
Interfaces
5 interfaces between chains.
- A–B · 644 Ų buried · 7 hydrogen bonds · protein-protein
- D–A · 452 Ų buried · 6 hydrogen bonds · protein-protein
- D–B · 339 Ų buried · 3 hydrogen bonds · protein-protein
- D–C · 214 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 182 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
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 7JXL · PDBe 7JXL · UniProt P00533
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